9OGR | pdb_00009ogr

Cryo-EM analysis of human H2A.Z on methylated Sat2R-P DNA (v1)

• PDB DOI: https://doi.org/10.2210/pdb9OGR/pdb
• NAKB: 9OGR
• EM Map EMD-70473: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21, Escherichia coli
• Mutation(s): No 


• Deposited: 2025-05-01 Released: 2025-11-05 
• Deposition Author(s): Shih, R.M., Arimura, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Impacts of DNA methylation on H2A.Z deposition and nucleosome stability

Shih, R.M., Arimura, Y., Konishi, H.A., Funabiki, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 202.47 kDa 
• Atom Count: 10,585 
• Modeled Residue Count: 947 
• Deposited Residue Count: 1,288 
• Unique protein chains: 4
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	136	Homo sapiens	Mutation(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 GTEx:  ENSG00000183598 ENSG00000203811 ENSG00000203852

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	Homo sapiens	Mutation(s): 0  Gene Names:  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
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.Z	C, G	127	Homo sapiens	Mutation(s): 0  Gene Names: H2AZ1, H2AFZ, H2AZ
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S5 (Homo sapiens) Explore P0C0S5  Go to UniProtKB:  P0C0S5
PHAROS:  P0C0S5 GTEx:  ENSG00000164032

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H	126	Homo sapiens	Mutation(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 ID: 5
Molecule	Chains	Length	Organism	Image
Methylated Sat2R-P DNA (124-MER)	I, J	152	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.78 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Shih, R.M., Arimura, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM132111

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release