9BE6 | pdb_00009be6

Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

Cryo-EM structure of Human Nucleosome collected by Leginon on Krios at 3.0 Angstrom resolution

Jia, L., Ruben, E.A., Olsen, S.K., Wasmuth, E.V.

To be published.

Macromolecule Content 

  • Total Structure Weight: 174.3 kDa 
  • Atom Count: 11,163 
  • Modeled Residue Count: 1,005 
  • Deposited Residue Count: 1,041 
  • Unique protein chains: 8
  • Unique nucleic acid chains: 2

Macromolecules


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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3.297Homo sapiensMutation(s): 0 
Gene Names: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens)
Explore Q71DI3 
Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3
Entity Groups
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UniProt GroupQ71DI3
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H483Homo sapiensMutation(s): 0 
UniProt
Find proteins for A0A9J8D176 (Cyprinus carpio carpio)
Explore A0A9J8D176 
Go to UniProtKB:  A0A9J8D176
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UniProt GroupA0A9J8D176
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1103Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S8 (Homo sapiens)
Explore P0C0S8 
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PHAROS:  P0C0S8
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UniProt GroupP0C0S8
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Reference Sequence
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|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B type 1-J95Homo sapiensMutation(s): 0 
Gene Names: H2BC11, H2BFR, HIST1H2BJ
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
PHAROS:  P06899
GTEx:  ENSG00000124635 
Entity Groups
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UniProt GroupP06899
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Reference Sequence
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|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3.297Homo sapiensMutation(s): 0 
Gene Names: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens)
Explore Q71DI3 
Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3
Entity Groups
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UniProt GroupQ71DI3
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Reference Sequence
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|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H478Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
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UniProt GroupP62805
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E105Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens)
Explore P04908 
Go to UniProtKB:  P04908
PHAROS:  P04908
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UniProt GroupP04908
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Reference Sequence
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|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B type 1-J93Homo sapiensMutation(s): 0 
Gene Names: H2BC11, H2BFR, HIST1H2BJ
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
Explore P06899 
Go to UniProtKB:  P06899
PHAROS:  P06899
GTEx:  ENSG00000124635 
Entity Groups
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UniProt GroupP06899
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Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff) 
Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (145-MER)145Homo sapiens
Sequence Annotations
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Reference Sequence
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(by identity cutoff) 
Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (145-MER)145Homo sapiens
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection