X-ray structure of the MMTV-A nucleosome core.

Abstract:

:The conformation of DNA bound in nucleosomes depends on the DNA sequence. Questions such as how nucleosomes are positioned and how they potentially bind sequence-dependent nuclear factors require near-atomic resolution structures of the nucleosome core containing different DNA sequences; despite this, only the DNA for two similar α-satellite sequences and a sequence (601) selected in vitro have been visualized bound in the nucleosome core. Here we report the 2.6-Å resolution X-ray structure of a nucleosome core particle containing the DNA sequence of nucleosome A of the 3'-LTR of the mouse mammary tumor virus (147 bp MMTV-A). To our knowledge, this is the first nucleosome core particle structure containing a promoter sequence and crystallized from Mg(2+) ions. It reveals sequence-dependent DNA conformations not seen previously, including kinking into the DNA major groove.

authors

Frouws TD,Duda SC,Richmond TJ

doi

10.1073/pnas.1524607113

subject

Has Abstract

pub_date

2016-02-02 00:00:00

pages

1214-9

issue

5

eissn

0027-8424

issn

1091-6490

pii

1524607113

journal_volume

113

pub_type

杂志文章
  • The p150Glued component of the dynactin complex binds to both microtubules and the actin-related protein centractin (Arp-1).

    abstract::p150Glued was first identified as a polypeptide that copurifies with cytoplasmic dynein, the minus-end-directed microtubule-based motor protein, and has more recently been shown to be present as a member of the oligomeric dynactin complex, which includes the actin-related protein centractin (Arp-1). Dynactin is though...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.5.1634

    authors: Waterman-Storer CM,Karki S,Holzbaur EL

    更新日期:1995-02-28 00:00:00

  • A generation at risk: young investigators and the future of the biomedical workforce.

    abstract::A number of distressing trends, including a decline in the share of key research grants going to younger scientists, as well as a steady rise in the age at which investigators receive their first funding, are now a decades-long feature of the US biomedical research workforce. Working committees have proposed recommend...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1418761112

    authors: Daniels RJ

    更新日期:2015-01-13 00:00:00

  • Cloning, expression, and genetic mapping of Sema W, a member of the semaphorin family.

    abstract::The semaphorins comprise a large family of membrane-bound and secreted proteins, some of which have been shown to function in axon guidance. We have cloned a transmembrane semaphorin, Sema W, that belongs to the class IV subgroup of the semaphorin family. The mouse and rat forms of Sema W show 97% amino acid sequence ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.5.2491

    authors: Encinas JA,Kikuchi K,Chedotal A,de Castro F,Goodman CS,Kimura T

    更新日期:1999-03-02 00:00:00

  • Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space.

    abstract::Over the last two decades, the number of gene/protein sequences gleaned from sequencing projects of individual genomes and environmental DNA has grown exponentially. Only a tiny fraction of these predicted proteins has been experimentally characterized, and the function of most proteins remains hypothetical or only pr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1815791116

    authors: Helbert W,Poulet L,Drouillard S,Mathieu S,Loiodice M,Couturier M,Lombard V,Terrapon N,Turchetto J,Vincentelli R,Henrissat B

    更新日期:2019-03-26 00:00:00

  • Disruption of Lrp4 function by genetic deletion or pharmacological blockade increases bone mass and serum sclerostin levels.

    abstract::We identified previously in vitro LRP4 (low-density lipoprotein receptor-related protein 4) as a facilitator of the WNT (Wingless-type) antagonist sclerostin and found mutations disrupting this function to be associated with high bone mass in humans similar to patients lacking sclerostin. To further delineate the role...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1413828111

    authors: Chang MK,Kramer I,Huber T,Kinzel B,Guth-Gundel S,Leupin O,Kneissel M

    更新日期:2014-12-02 00:00:00

  • An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis.

    abstract::HD domain phosphohydrolase enzymes are characterized by a conserved set of histidine and aspartate residues that coordinate an active site metallocenter. Despite the important roles these enzymes play in nucleotide metabolism and signal transduction, few have been both biochemically and structurally characterized. Her...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1613610113

    authors: Bridwell-Rabb J,Kang G,Zhong A,Liu HW,Drennan CL

    更新日期:2016-11-29 00:00:00

  • Noradrenergic blockade stabilizes prefrontal activity and enables fear extinction under stress.

    abstract::Stress-induced impairments in extinction learning are believed to sustain posttraumatic stress disorder (PTSD). Noradrenergic signaling may contribute to extinction impairments by modulating medial prefrontal cortex (mPFC) circuits involved in fear regulation. Here we demonstrate that aversive fear conditioning rapidl...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1500682112

    authors: Fitzgerald PJ,Giustino TF,Seemann JR,Maren S

    更新日期:2015-07-14 00:00:00

  • Cooperative DNA binding by CI repressor is dispensable in a phage lambda variant.

    abstract::Complex gene regulatory circuits contain many interacting components. In principle, all of these components and interactions may be essential to the function of the circuit. Alternatively, some of them may be refinements to a simpler version of the circuit that improve its fitness. In this work, we have tested whether...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0602223104

    authors: Babić AC,Little JW

    更新日期:2007-11-06 00:00:00

  • Maintenance of pre-mRNA secondary structure by epistatic selection.

    abstract::Linkage disequilibrium between polymorphisms in a natural population may result from various evolutionary forces, including random genetic drift due to sampling of gametes during reproduction, restricted migration between subpopulations in a subdivided population, or epistatic selection. In this report, we present evi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.20.9047

    authors: Kirby DA,Muse SV,Stephan W

    更新日期:1995-09-26 00:00:00

  • Site-specific genome editing for correction of induced pluripotent stem cells derived from dominant dystrophic epidermolysis bullosa.

    abstract::Genome editing with engineered site-specific endonucleases involves nonhomologous end-joining, leading to reading frame disruption. The approach is applicable to dominant negative disorders, which can be treated simply by knocking out the mutant allele, while leaving the normal allele intact. We applied this strategy ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1512028113

    authors: Shinkuma S,Guo Z,Christiano AM

    更新日期:2016-05-17 00:00:00

  • Assembly of Q{beta} viral RNA polymerase with host translational elongation factors EF-Tu and -Ts.

    abstract::Replication and transcription of viral RNA genomes rely on host-donated proteins. Qbeta virus infects Escherichia coli and replicates and transcribes its own genomic RNA by Qbeta replicase. Qbeta replicase requires the virus-encoded RNA-dependent RNA polymerase (beta-subunit), and the host-donated translational elonga...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1006559107

    authors: Takeshita D,Tomita K

    更新日期:2010-09-07 00:00:00

  • Local demographic changes and US presidential voting, 2012 to 2016.

    abstract::Immigration and demographic change have become highly salient in American politics, partly because of the 2016 campaign of Donald Trump. Previous research indicates that local influxes of immigrants or unfamiliar ethnic groups can generate threatened responses, but has either focused on nonelectoral outcomes or analyz...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1909202116

    authors: Hill SJ,Hopkins DJ,Huber GA

    更新日期:2019-12-10 00:00:00

  • Observations and interpretation of x-ray absorption edges in iron compounds and proteins.

    abstract::X-ray absorption spectra near the Kalpha edge have been measured in various iron group compounds using the intense synchrotron radiation at the Stanford Synchrotron Research Project. In the cubic compounds KMF3 where M = Mn+2, Fe+2, Co+2, Ni+2, and Zn+2, well resolved lines were observed and assigned to the 1s leads t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.73.5.1384

    authors: Shulman GR,Yafet Y,Eisenberger P,Blumberg WE

    更新日期:1976-05-01 00:00:00

  • Monophyletic origin of beta-division proteobacterial endosymbionts and their coevolution with insect trypanosomatid protozoa Blastocrithidia culicis and Crithidia spp.

    abstract::Some trypanosomatid protozoa (order Kinetoplastida) are well known to harbor bacterial endosymbionts. Their phylogenetic positions and evolutionary relationships with the hosts were deduced by comparing the rRNA gene sequences. Earlier, we observed that these symbionts from three Crithidia spp. are identical and are c...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.18.8437

    authors: Du Y,Maslov DA,Chang KP

    更新日期:1994-08-30 00:00:00

  • Activated Cdc42-associated kinase Ack1 promotes prostate cancer progression via androgen receptor tyrosine phosphorylation.

    abstract::Activation of the androgen receptor (AR) may play a role in androgen-independent progression of prostate cancer. Multiple mechanisms of AR activation, including stimulation by tyrosine kinases, have been postulated. We and others have recently shown involvement of activated Cdc42-associated tyrosine kinase Ack1 in adv...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0700420104

    authors: Mahajan NP,Liu Y,Majumder S,Warren MR,Parker CE,Mohler JL,Earp HS,Whang YE

    更新日期:2007-05-15 00:00:00

  • Antibodies mediate intracellular immunity through tripartite motif-containing 21 (TRIM21).

    abstract::Antibodies provide effective antiviral immunity despite the fact that viruses escape into cells when they infect. Here we show that antibodies remain attached to viruses after cell infection and mediate an intracellular immune response that disables virions in the cytosol. We have discovered that cells possess a cytos...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1014074107

    authors: Mallery DL,McEwan WA,Bidgood SR,Towers GJ,Johnson CM,James LC

    更新日期:2010-11-16 00:00:00

  • DNA nucleotide excision repair-dependent signaling to checkpoint activation.

    abstract::Eukaryotic cells respond to a variety of DNA insults by triggering a common signal transduction cascade, known as checkpoint response, which temporarily halts cell-cycle progression. Although the main players involved in the cascade have been identified, there is still uncertainty about the nature of the structures th...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0605446103

    authors: Marini F,Nardo T,Giannattasio M,Minuzzo M,Stefanini M,Plevani P,Muzi Falconi M

    更新日期:2006-11-14 00:00:00

  • Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice.

    abstract::Defining prospective pathways by which zoonoses evolve and emerge as human pathogens is critical for anticipating and controlling both natural and deliberate pandemics. However, predicting tenable pathways of animal-to-human movement has been hindered by challenges in identifying reservoir species, cultivating zoonoti...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0808116105

    authors: Becker MM,Graham RL,Donaldson EF,Rockx B,Sims AC,Sheahan T,Pickles RJ,Corti D,Johnston RE,Baric RS,Denison MR

    更新日期:2008-12-16 00:00:00

  • Insulin binding and insulin action in cultured fibroblasts: significant differences between a phosphoglucose isomerase-deficient mutant and the parental strain.

    abstract::The interrelationships of hexose feeding and insulin action were studied in the Chinese hamster fibroblast cell lines 023 and DS-7. The latter, derived from 023 and deficient in phosphoglucose isomerase, has been used to map the metabolic requirements for aldohexose-mediated down-regulation or "curbing" of hexose tran...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.11.3684

    authors: Wilson C,Peterson SW,Ullrey DB,Kalckar HM

    更新日期:1986-06-01 00:00:00

  • DNA supercoiling affects in vitro transcription of two maize chloroplast genes differently.

    abstract::Two adjacent, divergently transcribed, developmentally regulated genes of the maize chloroplast chromosome have different superhelical density/transcriptional activation profiles when transcribed in vitro by the homologous DNA-dependent RNA polymerase. Promoter-specific transcription of the gene for the beta and epsil...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.82.15.4886

    authors: Stirdivant SM,Crossland LD,Bogorad L

    更新日期:1985-08-01 00:00:00

  • Sigma-1 receptor regulates Tau phosphorylation and axon extension by shaping p35 turnover via myristic acid.

    abstract::Dysregulation of cyclin-dependent kinase 5 (cdk5) per relative concentrations of its activators p35 and p25 is implicated in neurodegenerative diseases. P35 has a short t½ and undergoes rapid proteasomal degradation in its membrane-bound myristoylated form. P35 is converted by calpain to p25, which, along with an exte...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1422001112

    authors: Tsai SY,Pokrass MJ,Klauer NR,Nohara H,Su TP

    更新日期:2015-05-26 00:00:00

  • Reductive detoxification as a mechanism of fungal resistance to singlet oxygen-generating photosensitizers.

    abstract::Fungi that are resistant or sensitive to the singlet oxygen-generating toxin cercosporin were assayed for their ability to detoxify it by reduction. Cercosporin reduction was assayed microscopically by using bandpass filters to differentiate between fluorescence emission from cercosporin and reduced cercosporin. Hypha...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.20.9588

    authors: Daub ME,Leisman GB,Clark RA,Bowden EF

    更新日期:1992-10-15 00:00:00

  • Acidity across the interface from the ocean surface to sea spray aerosol.

    abstract::Aerosols impact climate, human health, and the chemistry of the atmosphere, and aerosol pH plays a major role in the physicochemical properties of the aerosol. However, there remains uncertainty as to whether aerosols are acidic, neutral, or basic. In this research, we show that the pH of freshly emitted (nascent) sea...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2018397118

    authors: Angle KJ,Crocker DR,Simpson RMC,Mayer KJ,Garofalo LA,Moore AN,Mora Garcia SL,Or VW,Srinivasan S,Farhan M,Sauer JS,Lee C,Pothier MA,Farmer DK,Martz TR,Bertram TH,Cappa CD,Prather KA,Grassian VH

    更新日期:2021-01-12 00:00:00

  • Human thioredoxin reductase from HeLa cells: selective alkylation of selenocysteine in the protein inhibits enzyme activity and reduction with NADPH influences affinity to heparin.

    abstract::Human thioredoxin reductase (TR) contains selenocysteine (Secys) in a redox center [cysteine (Cys)-497,Secys-498] near the C-terminus. The essential role of Secys in TR isolated from HeLa cells was demonstrated by the alkylation studies. Reaction of native NADPH reduced enzyme with bromoacetate at pH 6.5 inhibited enz...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.15.8520

    authors: Gorlatov SN,Stadtman TC

    更新日期:1998-07-21 00:00:00

  • Selection for Staphylococcus aureus small-colony variants due to growth in the presence of Pseudomonas aeruginosa.

    abstract::Opportunistic infections are often polymicrobial. Two of the most important bacterial opportunistic pathogens of humans, Pseudomonas aeruginosa and Staphylococcus aureus, frequently are coisolated from infections of catheters, endotracheal tubes, skin, eyes, and the respiratory tract, including the airways of people w...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0606756104

    authors: Hoffman LR,Déziel E,D'Argenio DA,Lépine F,Emerson J,McNamara S,Gibson RL,Ramsey BW,Miller SI

    更新日期:2006-12-26 00:00:00

  • Biphasic regulation of InsP3 receptor gating by dual Ca2+ release channel BH3-like domains mediates Bcl-xL control of cell viability.

    abstract::Antiapoptotic Bcl-2 family members interact with inositol trisphosphate receptor (InsP3R) Ca(2+)release channels in the endoplasmic reticulum to modulate Ca(2+)signals that affect cell viability. However, the molecular details and consequences of their interactions are unclear. Here, we found that Bcl-xL activates sin...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1517935113

    authors: Yang J,Vais H,Gu W,Foskett JK

    更新日期:2016-03-29 00:00:00

  • Structure of the human renin gene.

    abstract::The human renin gene was isolated from a Charon 4A human genomic library and characterized. The gene spans about 11.7 kilobases and consists of 10 exons and 9 introns that map at points that could be variable surface loops of the enzyme. The complete coding regions, the 5'- and 3'-flanking regions, and the exon-intron...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.81.19.5999

    authors: Miyazaki H,Fukamizu A,Hirose S,Hayashi T,Hori H,Ohkubo H,Nakanishi S,Murakami K

    更新日期:1984-10-01 00:00:00

  • Labeled cortical mantle distance maps of the cingulate quantify differences between dementia of the Alzheimer type and healthy aging.

    abstract::The cingulate gyri in 37 subjects with and without early dementia of the Alzheimer type (DAT) were studied by using MRI at 1.0 mm3 isotropic resolution. Groups were segregated into young controls (n = 10), age-matched normal controls (n = 10), very mild DAT (n = 8), and mild DAT (n = 9). By using automated Bayesian se...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2136624100

    authors: Miller MI,Hosakere M,Barker AR,Priebe CE,Lee N,Ratnanather JT,Wang L,Gado M,Morris JC,Csernansky JG

    更新日期:2003-12-09 00:00:00

  • Selective presynaptic enhancement of the prefrontal cortex to nucleus accumbens pathway by cocaine.

    abstract::The nucleus accumbens (NAc) regulates motivated behavior by, in part, processing excitatory synaptic projections from several brain regions. Among these regions, the prefrontal cortex (PFC) and basolateral amygdala, convey executive control and affective states, respectively. Whereas glutamatergic synaptic transmissio...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1206287110

    authors: Suska A,Lee BR,Huang YH,Dong Y,Schlüter OM

    更新日期:2013-01-08 00:00:00

  • Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein.

    abstract::Numerous relatively short regions within intrinsically disordered proteins (IDPs) serve as molecular recognition elements (MoREs). They fold into ordered structures upon binding to their partner molecules. Currently, there is still a lack of in-depth understanding of how coupled binding and folding occurs in MoREs. He...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1308381110

    authors: Wang Y,Chu X,Longhi S,Roche P,Han W,Wang E,Wang J

    更新日期:2013-10-01 00:00:00