8YTH

Crystal structures of human IRF2BP2 RING domain in complex with ZBTB16 peptide

• PDB DOI: https://doi.org/10.2210/pdb8YTH/pdb

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


• Deposited: 2024-03-25 Released: 2024-11-20 
• Deposition Author(s): Wang, G.C., Ding, J.P.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.281 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 

Starting Model: experimental

Literature

IRF2BP2 recognizes and bind to a conserved RxSVI sequence motif of protein partners and interacts with ZBTB16 to regulate megakaryocytic differentiation

Wang, G.C., Ding, J.P.

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)

Macromolecule Content

• Total Structure Weight: 9.88 kDa 
• Atom Count: 561 
• Modelled Residue Count: 76 
• Deposited Residue Count: 91 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon regulatory factor 2-binding protein 2	A	83	Homo sapiens	Mutation(s): 0  Gene Names: IRF2BP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z5L9 (Homo sapiens) Explore Q7Z5L9  Go to UniProtKB:  Q7Z5L9
PHAROS:  Q7Z5L9 GTEx:  ENSG00000168264

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger and BTB domain-containing protein 16	B	8	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q05516 (Homo sapiens) Explore Q05516  Go to UniProtKB:  Q05516
PHAROS:  Q05516 GTEx:  ENSG00000109906

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.281 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.315	α = 90
b = 47.315	β = 90
c = 57.489	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Wang, G.C., Ding, J.P.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB37030305

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release