9V5M | pdb_00009v5m

The crystal structure of RBBP4-H3 complex

• PDB DOI: https://doi.org/10.2210/pdb9V5M/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, synthetic construct
• Mutation(s): No 


• Deposited: 2025-05-26 Released: 2026-06-03 
• Deposition Author(s): Zhang, M., Wang, X.X., He, X.Y., Zang, J.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of RBBP4-H3 complex

Zhang, M., Wang, X.X., He, X.Y., Zang, J.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.45 kDa 
• Atom Count: 3,520 
• Modeled Residue Count: 415 
• Deposited Residue Count: 439 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-binding protein RBBP4	A	425	Homo sapiens	Mutation(s): 0  Gene Names: RBBP4, RBAP48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09028 (Homo sapiens) Explore Q09028  Go to UniProtKB:  Q09028
PHAROS:  Q09028 GTEx:  ENSG00000162521

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3C	B [auth D]	14	Homo sapiens	Mutation(s): 0  Gene Names: H3-5, H3F3C
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NXT2 (Homo sapiens) Explore Q6NXT2  Go to UniProtKB:  Q6NXT2
PHAROS:  Q6NXT2 GTEx:  ENSG00000188375

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTN	C [auth D]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.01	α = 90
b = 77.463	β = 90.61
c = 64.301	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Zhang, M., Wang, X.X., He, X.Y., Zang, J.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32401008

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release