9XVD | pdb_00009xvd

Crystal structure of NFIC homodimer bound to DNA

• PDB DOI: https://doi.org/10.2210/pdb9XVD/pdb

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-11-26 Released: 2025-12-31 
• Deposition Author(s): Pan, S.L., Min, J.R., Liu, K.
• 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: 
  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NFIC homodimer bound to DNA

Pan, S.L., Min, J.R., Liu, K.

To be published.

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: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 117.65 kDa 
• Atom Count: 7,542 
• Modeled Residue Count: 773 
• Deposited Residue Count: 876 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear factor 1 C-type	A, B [auth C], C [auth B], D	198	Homo sapiens	Mutation(s): 0  Gene Names: NFIC, NFI
UniProt & NIH Common Fund Data Resources
Find proteins for P08651 (Homo sapiens) Explore P08651  Go to UniProtKB:  P08651
PHAROS:  P08651 GTEx:  ENSG00000141905

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*GP*TP*TP*GP*GP*CP*AP*CP*CP*GP*TP*GP*CP*CP*AP*AP*CP*TP*T)-3')	E, G	21	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*GP*TP*TP*GP*GP*CP*AP*CP*GP*GP*TP*GP*CP*CP*AP*AP*CP*TP*T)-3')	F, H	21	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	J [auth A], K [auth C], M [auth B], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	I [auth A], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.254 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.457	α = 90
b = 84.29	β = 90
c = 146.71	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Pan, S.L., Min, J.R., Liu, K.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32371328

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release