8HCU

Crystal structure of BCOR/PCGF1/KDM2B complex

• PDB DOI: https://doi.org/10.2210/pdb8HCU/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-11-03 Released: 2023-11-15 
• Deposition Author(s): Shen, F., Chen, R., Xu, J., Liu, J.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.238 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 

Literature

Crystal structure of BCOR/PCGF1/KDM2B complex

Shen, F., Chen, R., Xu, J., Liu, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 55.32 kDa 
• Atom Count: 3,592 
• Modelled Residue Count: 438 
• Deposited Residue Count: 482 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cDNA FLJ55590, highly similar to JmjC domain-containing histone demethylation protein 1B	A	235	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NHM5 (Homo sapiens) Explore Q8NHM5  Go to UniProtKB:  Q8NHM5
PHAROS:  Q8NHM5 GTEx:  ENSG00000089094

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb group RING finger protein 1	B	105	Homo sapiens	Mutation(s): 0  Gene Names: PCGF1, NSPC1, RNF68
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BSM1 (Homo sapiens) Explore Q9BSM1  Go to UniProtKB:  Q9BSM1
PHAROS:  Q9BSM1 GTEx:  ENSG00000115289

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BCL-6 corepressor	C	142	Homo sapiens	Mutation(s): 0  Gene Names: BCOR, KIAA1575
UniProt & NIH Common Fund Data Resources
Find proteins for Q6W2J9 (Homo sapiens) Explore Q6W2J9  Go to UniProtKB:  Q6W2J9
PHAROS:  Q6W2J9 GTEx:  ENSG00000183337

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY (Subject of Investigation/LOI)	D [auth A], E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.238 
• R-Value Work: 0.200 
• R-Value Observed: 0.202 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.291	α = 90
b = 67.291	β = 90
c = 252.035	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-15 
Deposition Author(s): Shen, F., Chen, R., Xu, J., Liu, J.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2017YFA0504104

Revision History  

• Version 1.0: 2023-11-15
  Type: Initial release