6U9Q

Crystal Structure Analysis of DNA-BCL11A Znf domain complex

• PDB DOI: https://doi.org/10.2210/pdb6U9Q/pdb
• NAKB: 6U9Q

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


• Deposited: 2019-09-09 Released: 2020-09-16 
• Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.195 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

Structural insights into the DNA-binding mechanism of BCL11A: The integral role of ZnF6

Viennet, T., Yin, M., Jayaraj, A., Kim, W., Sun, Z.Y.J., Fujiwara, Y., Zhang, K., Seruggia, D., Seo, H.S., Dhe-Paganon, S., Orkin, S.H., Arthanari, H.

(2024) Structure 

• DOI: https://doi.org/10.1016/j.str.2024.09.022

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

Macromolecule Content

• Total Structure Weight: 21.11 kDa 
• Atom Count: 1,329 
• Modelled Residue Count: 115 
• Deposited Residue Count: 136 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-cell lymphoma/leukemia 11A	A	110	Homo sapiens	Mutation(s): 0  Gene Names: BCL11A, CTIP1, EVI9, KIAA1809, ZNF856
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H165 (Homo sapiens) Explore Q9H165  Go to UniProtKB:  Q9H165
PHAROS:  Q9H165 GTEx:  ENSG00000119866

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA5	B	13	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA3	C	13	Homo sapiens

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	D [auth A], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.195 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101	α = 90
b = 60.16	β = 129.73
c = 75.79	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Seo, H.-S., Dhe-Paganon, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references
• Version 1.2: 2024-10-23
  Changes: Database references, Structure summary