8UXQ

Structure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome

• PDB DOI: https://doi.org/10.2210/pdb8UXQ/pdb
• EM Map EMD-42774: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Homo sapiens, Xenopus laevis, Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-11-09 Released: 2024-09-25 
• Deposition Author(s): Tan, D., Sokolova, V.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structure of human HP1 in complex with H2A.Z nucleosome

Tan, D., Sokolova, V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B2C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - B2C2D2E2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - B2C2D2E2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 281.48 kDa 
• Atom Count: 12,603 
• Modelled Residue Count: 1,276 
• Deposited Residue Count: 1,784 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromobox protein homolog 5	A, B [auth C]	195	Homo sapiens	Mutation(s): 0  Gene Names: CBX5, HP1A
UniProt & NIH Common Fund Data Resources
Find proteins for P45973 (Homo sapiens) Explore P45973  Go to UniProtKB:  P45973
PHAROS:  P45973 GTEx:  ENSG00000094916

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	C [auth E], G [auth K]	135	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth F], H [auth L]	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.Z	E [auth G], I [auth M]	127	Mus musculus	Mutation(s): 0  Gene Names: H2az1, H2afz, H2az
UniProt & NIH Common Fund Data Resources
Find proteins for P0C0S6 (Mus musculus) Explore P0C0S6  Go to UniProtKB:  P0C0S6
IMPC:  MGI:1888388

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	F [auth H], J [auth N]	125	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA Widom601 (208bp) strand1	K [auth I]	208	synthetic construct

Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA Widom601 (208bp) strand2	L [auth J]	208	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	MDFF
RECONSTRUCTION	RELION	4.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Tan, D., Sokolova, V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM133611
National Science Foundation (NSF, United States)	United States	1942049

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release