9A9W | pdb_00009a9w

USP7 bound to a nucleosome/p53 complex

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.

PDB DOI: https://doi.org/10.2210/pdb9A9W/pdb
NAKB: 9A9W

Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2025-04-29 Released: 2025-08-06
Deposition Author(s): Chakraborty, D., Kempf, G., Kater, L., Cavadini, S., Thoma, N.H.

Integrative Structure Snapshot

Multi-Scale: No
Multi-State: No
Ordered-State: No
Deposited Models: 1
Representative Model: 1

wwPDB ValidationFull ReportSummary Report

This is version 1.0 of the entry. See complete history.

Literature

Nucleosomes specify co-factor access to p53

Chakraborty, D., Sandate, C.R., Isbel, L., Kempf, G., Weiss, J., Cavadini, S., Kater, L., Seebacher, J., Kozicka, Z., Stoos, L., Grand, R.S., Schubeler, D., Michael, A.K., Thoma, N.H.

(2025) Mol Cell

DOI: https://doi.org/10.1016/j.molcel.2025.06.027

Macromolecule Content

Total Structure Weight: 597.76 kDa
Atom Count: 27,042
Modeled Residue Count: 2,978
Deposited Residue Count: 4,112
Unique protein chains: 6
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	A, E	139	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431 GTEx: ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	106	N/A	Mutation(s): 0
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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62805
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	133	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908 Go to UniProtKB: P04908
PHAROS: P04908 GTEx: ENSG00000277075 ENSG00000278463
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04908
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	128	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899 Go to UniProtKB: P06899
PHAROS: P06899 GTEx: ENSG00000124635
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06899
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular tumor antigen p53	K, L, M, N	417	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637 Go to UniProtKB: P04637
PHAROS: P04637 GTEx: ENSG00000141510
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04637
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 7	O	1,126	N/A	Mutation(s): 0 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens) Explore Q93009 Go to UniProtKB: Q93009
PHAROS: Q93009 GTEx: ENSG00000187555
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q93009
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
DNA 153-mer	I	153	N/A
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
DNA 153-mer	J	153	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain S SDF format, chain R SDF format, chain Q SDF format, chain P MOL2 format, chain S MOL2 format, chain R MOL2 format, chain Q MOL2 format, chain P mmCIF format, chain S mmCIF format, chain R mmCIF format, chain Q mmCIF format, chain P	P, Q, R, S	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain P Focus chain Q Focus chain R Focus chain S