8JQ0 | pdb_00008jq0

Crystal structure of ZBTB48 ZF10-11-C in complex with CIITA promoter

• PDB DOI: https://doi.org/10.2210/pdb8JQ0/pdb
• NAKB: 8JQ0

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-06-13 Released: 2024-12-18 
• Deposition Author(s): Li, F.D., Wang, S.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.291 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.233 (Depositor) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ZBTB48 ZF10-11-C in complex with CIITA promoter

Li, F.D., Wang, S.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 37.93 kDa 
• Atom Count: 2,476 
• Modeled Residue Count: 200 
• Deposited Residue Count: 210 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HKR3 protein	A, D	73	Homo sapiens	Mutation(s): 0  Gene Names: HKR3
UniProt
Find proteins for Q6LCP1 (Homo sapiens) Explore Q6LCP1  Go to UniProtKB:  Q6LCP1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*CP*AP*AP*GP*TP*GP*AP*GP*GP*GP*AP*TP*CP*A)-3')	B, E	16	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*GP*AP*TP*CP*CP*CP*TP*CP*AP*CP*TP*TP*GP*T)-3')	C, F	16	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth A], I [auth D], J [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.291 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.233 (Depositor) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.563	α = 90
b = 46.864	β = 124.89
c = 79.047	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: 2024-12-18 
Deposition Author(s): Li, F.D., Wang, S.M.

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

Revision History  

• Version 1.0: 2024-12-18
  Type: Initial release