7BWD | pdb_00007bwd

Structure of Dot1L-H2BK34ub Nucleosome Complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7BWD

This is version 1.2 of the entry. See complete history. 

Literature

Structure of the Dot1L-H2BK34ub Nucleosome Complex Reveals an Unprecedented Crosstalk Activation Mechanism through Nucleosome Shape Distortion

Liu, L., Lou, Z.Y., Ai, H.S., Cao, L.

To be published.

Macromolecule Content 

  • Total Structure Weight: 264.05 kDa 
  • Atom Count: 16,042 
  • Modeled Residue Count: 1,548 
  • Deposited Residue Count: 1,842 
  • Unique protein chains: 6
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-79 specificA [auth K]416Homo sapiensMutation(s): 0 
Gene Names: DOT1L, KIAA1814, KMT4
EC: 2.1.1.360
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEK3 (Homo sapiens)
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Go to UniProtKB:  Q8TEK3
PHAROS:  Q8TEK3
GTEx:  ENSG00000104885 
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UniProt GroupQ8TEK3
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H4B [auth F],
I [auth B]		102Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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UniProt GroupP62805
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/EC [auth G],
H [auth C]		129Homo sapiensMutation(s): 0 
Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
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Find proteins for P04908 (Homo sapiens)
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PHAROS:  P04908
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H2B type 1-KD [auth H],
G [auth D]		125Homo sapiensMutation(s): 0 
Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens)
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PHAROS:  O60814
GTEx:  ENSG00000197903 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3.1E,
F [auth A]		135Homo sapiensMutation(s): 0 
Gene Names: 
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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin
L, M
76Homo sapiensMutation(s): 1 
Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens)
Explore P62979 
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PHAROS:  P62979
GTEx:  ENSG00000143947 
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Reference Sequence
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (146-MER)J [auth I]146Homo sapiens
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Reference Sequence
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (146-MER)K [auth J]146Homo sapiens
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH

Query on SAH


Download:Ideal Coordinates CCD File
N [auth K]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0505200
National Natural Science Foundation of China (NSFC)China21532004
National Natural Science Foundation of China (NSFC)China91753205
National Natural Science Foundation of China (NSFC)China81621002

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-14
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-06-18
    Changes: Advisory, Data collection, Derived calculations