8YDD | pdb_00008ydd

Crystal structure of Nanog(R100A) in complex with Wdr5

• PDB DOI: https://doi.org/10.2210/pdb8YDD/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-02-20 Released: 2025-03-26 
• Deposition Author(s): Wang, D., Shi, X., Zhao, L., Wu, B., Chen, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of Nanog(R100A) in complex with Wdr5

Wang, D., Shi, X., Zhao, L., Wu, B., Chen, Y., Li, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 118.06 kDa 
• Atom Count: 8,454 
• Modeled Residue Count: 1,024 
• Deposited Residue Count: 1,061 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A, B, C	313	Mus musculus	Mutation(s): 0  Gene Names: Wdr5, Big, Big3
UniProt
Find proteins for P61965 (Mus musculus) Explore P61965  Go to UniProtKB:  P61965

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein NANOG	D, E	61	Mus musculus	Mutation(s): 1  Gene Names: Nanog, Ecat4, Enk
UniProt
Find proteins for Q80Z64 (Mus musculus) Explore Q80Z64  Go to UniProtKB:  Q80Z64

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.667	α = 90
b = 87.604	β = 91.81
c = 96.874	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Wang, D., Shi, X., Zhao, L., Wu, B., Chen, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31670748
National Natural Science Foundation of China (NSFC)	China	31970576
National Natural Science Foundation of China (NSFC)	China	32071195
National Natural Science Foundation of China (NSFC)	China	31900934

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release