[English] 日本語
Yorodumi
- PDB-6buz: Cryo-EM structure of CENP-A nucleosome in complex with kinetochor... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6buz
TitleCryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N
Components
  • (DNA (147-MER)) x 2
  • Histone H2A
  • Histone H2B
  • Histone H3-like centromeric protein A
  • Histone H4
  • Maltose-binding periplasmic protein, Centromere protein N chimera
KeywordsSTRUCTURAL PROTEIN/DNA / STRUCTURAL PROTEIN-DNA complex / Histone fold / Centromeric nucleosome / Kinetochore
Function / homologySolute-binding family 1, conserved site / Packaging Of Telomere Ends / Histone H4 signature. / Histone H2B signature. / Histone H3 signature 2. / Bacterial extracellular solute-binding proteins, family 1 signature. / Meiotic synapsis / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Pre-NOTCH Transcription and Translation / C-terminus of histone H2A ...Solute-binding family 1, conserved site / Packaging Of Telomere Ends / Histone H4 signature. / Histone H2B signature. / Histone H3 signature 2. / Bacterial extracellular solute-binding proteins, family 1 signature. / Meiotic synapsis / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Pre-NOTCH Transcription and Translation / C-terminus of histone H2A / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Separation of Sister Chromatids / Resolution of Sister Chromatid Cohesion / Oxidative Stress Induced Senescence / Histone H2A signature. / Centromere kinetochore component CENP-T histone fold / DNA Damage/Telomere Stress Induced Senescence / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Histone H2A, C-terminal domain / Histone H4, conserved site / Histone-fold / Centromere protein Chl4/mis15/CENP-N / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / TATA box binding protein associated factor (TAF) / Histone H2A / Histone H4 / Histone H2B / Histone H3/CENP-A / Kinetochore protein CHL4 like / CENP-T/Histone H4, histone fold / Senescence-Associated Secretory Phenotype (SASP) / HDACs deacetylate histones / RNA Polymerase I Promoter Opening / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / G2/M DNA damage checkpoint / RNA Polymerase I Chain Elongation / Metalloprotease DUBs / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Estrogen-dependent gene expression / Meiotic recombination / Amyloid fiber formation / PKMTs methylate histone lysines / Histone H2A conserved site / Ub-specific processing proteases / UCH proteinases / HDMs demethylate histones / HATs acetylate histones / RMTs methylate histone arginines / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / NoRC negatively regulates rRNA expression / SUMOylation of chromatin organization proteins / B-WICH complex positively regulates rRNA expression / DNA methylation / Transcriptional regulation by small RNAs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RHO GTPases Activate Formins / condensed chromosome inner kinetochore / kinetochore assembly / protein localization to chromosome, centromeric region / condensed nuclear chromosome kinetochore / nuclear pericentric heterochromatin / establishment of mitotic spindle orientation / negative regulation of megakaryocyte differentiation / CENP-A containing nucleosome assembly / condensed nuclear chromosome, centromeric region / DNA replication-independent nucleosome assembly / chromatin silencing / telomere capping / condensed chromosome kinetochore / chromosome, centromeric region / negative regulation of tumor necrosis factor-mediated signaling pathway / carbohydrate transmembrane transporter activity / innate immune response in mucosa / mitotic cytokinesis / telomere organization / DNA replication-dependent nucleosome assembly / nucleosomal DNA binding / nuclear nucleosome / regulation of gene silencing by miRNA / chromatin silencing at rDNA / negative regulation of gene expression, epigenetic / DNA-templated transcription, initiation / nuclear chromosome / regulation of megakaryocyte differentiation / chromosome segregation / nucleosome / lipopolysaccharide binding
Function and homology information
Specimen sourceHomo sapiens (human)
Escherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.92 Å resolution
AuthorsChittori, S. / Hong, J. / Kelly, A.E. / Bai, Y. / Subramaniam, S.
CitationJournal: Science / Year: 2018
Title: Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N.
Authors: Sagar Chittori / Jingjun Hong / Hayden Saunders / Hanqiao Feng / Rodolfo Ghirlando / Alexander E Kelly / Yawen Bai / Sriram Subramaniam
Abstract: Accurate chromosome segregation requires the proper assembly of kinetochore proteins. A key step in this process is the recognition of the histone H3 variant CENP-A in the centromeric nucleosome by ...Accurate chromosome segregation requires the proper assembly of kinetochore proteins. A key step in this process is the recognition of the histone H3 variant CENP-A in the centromeric nucleosome by the kinetochore protein CENP-N. We report cryo-electron microscopy (cryo-EM), biophysical, biochemical, and cell biological studies of the interaction between the CENP-A nucleosome and CENP-N. We show that human CENP-N confers binding specificity through interactions with the L1 loop of CENP-A, stabilized by electrostatic interactions with the nucleosomal DNA. Mutational analyses demonstrate analogous interactions in , which are further supported by residue-swapping experiments involving the L1 loop of CENP-A. Our results are consistent with the coevolution of CENP-N and CENP-A and establish the structural basis for recognition of the CENP-A nucleosome to enable kinetochore assembly and centromeric chromatin organization.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 11, 2017 / Release: Dec 20, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 20, 2017Structure modelrepositoryInitial release
1.1Jan 10, 2018Structure modelDatabase referencescitation_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.2Jan 31, 2018Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7293
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone H3-like centromeric protein A
B: Histone H4
C: Histone H2A
D: Histone H2B
E: Histone H3-like centromeric protein A
F: Histone H4
G: Histone H2A
H: Histone H2B
I: DNA (147-MER)
J: DNA (147-MER)
N: Maltose-binding periplasmic protein, Centromere protein N chimera


Theoretical massNumber of molelcules
Total (without water)281,73711
Polyers281,73711
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Sedimentation Velocity
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)54640
ΔGint (kcal/M)-395
Surface area (Å2)84880

-
Components

-
Protein/peptide , 5 types, 9 molecules AEBFCGDHN

#1: Protein/peptide Histone H3-like centromeric protein A / Centromere autoantigen A / Centromere protein A / CENP-A


Mass: 18195.002 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: CENPA / Production host: Escherichia coli (E. coli) / References: UniProt: P49450
#2: Protein/peptide Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein/peptide Histone H2A / / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14165.551 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein/peptide Histone H2B / / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13935.239 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#7: Protein/peptide Maltose-binding periplasmic protein, Centromere protein N chimera / MBP / MMBP / Maltodextrin-binding protein / CENP-N / Interphase centromere complex protein 32


Mass: 75607.797 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, CENPN, C16orf60, ICEN32, BM-309 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEY0, UniProt: Q96H22

-
DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (147-MER)


Mass: 45138.770 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (147-MER)


Mass: 45610.043 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Centromeric nucleosome in complex with kinetochore protein CENP-N
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
12RELION2.03D reconstruction
19PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 61749 / Symmetry type: POINT
Atomic model buildingDetails: Ab initio modeling of CENP-N backbone trace / Ref protocol: OTHER / Ref space: REAL / Target criteria: Model to Map correlation, Molprobity
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00813311
ELECTRON MICROSCOPYf_angle_d0.85819246
ELECTRON MICROSCOPYf_dihedral_angle_d24.3466952
ELECTRON MICROSCOPYf_chiral_restr0.0472216
ELECTRON MICROSCOPYf_plane_restr0.0051438

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more