7XV7

Crystal structure of ZYG11B bound to ORF10 peptide

• PDB DOI: https://doi.org/10.2210/pdb7XV7/pdb

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


• Deposited: 2022-05-21 Released: 2022-06-08 
• Deposition Author(s): Dong, C., Yan, X., Li, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.269 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Literature

Structural insights into ORF10 recognition by ZYG11B

Zhang, B., Li, Y., Feng, Q., Song, L., Dong, C., Yan, X.

(2022) Biochem Biophys Res Commun 616: 14-18

• DOI: https://doi.org/10.1016/j.bbrc.2022.05.069

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 57.37 kDa 
• Atom Count: 3,988 
• Modelled Residue Count: 490 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein zyg-11 homolog B	A [auth B], B [auth A]	250	Homo sapiens	Mutation(s): 0  Gene Names: ZYG11B, KIAA1730
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C0D3 (Homo sapiens) Explore Q9C0D3  Go to UniProtKB:  Q9C0D3
PHAROS:  Q9C0D3 GTEx:  ENSG00000162378

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.269 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.504	α = 90
b = 96.854	β = 90
c = 121.749	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Dong, C., Yan, X., Li, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31900865
National Natural Science Foundation of China (NSFC)	China	32071193
National Natural Science Foundation of China (NSFC)	China	81874039

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description