6KI6 | pdb_00006ki6

Crystal structure of BCL11A in complex with gamma-globin -115 HPFH region

• PDB DOI: https://doi.org/10.2210/pdb6KI6/pdb
• NAKB: 6KI6

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


• Deposited: 2019-07-17 Released: 2019-09-11 
• Deposition Author(s): Li, F.D., Yang, Y., Shi, Y.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.251 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.207 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Structural insights into the recognition of gamma-globin gene promoter by BCL11A.

Yang, Y., Xu, Z., He, C., Zhang, B., Shi, Y., Li, F.

(2019) Cell Res 29: 960-963

• PubMed: 31467406 
• DOI: https://doi.org/10.1038/s41422-019-0221-0
• Primary Citation Related Structures: 
  6KI6

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Organizational Affiliation: 
• Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026, Hefei, Anhui, China.
Anhui Key Laboratory of Modern Biomanufacturing and School of Life Sciences, Anhui University, 230601, Hefei, Anhui, China.
Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026, Hefei, Anhui, China. [e-mail].
Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026, Hefei, Anhui, China. [e-mail].

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: 41.5 kDa 
• Atom Count: 2,179 
• Modeled Residue Count: 185 
• Deposited Residue Count: 270 
• 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, B	109	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
DNA (5'-D(*AP*TP*AP*TP*TP*GP*GP*TP*CP*AP*AP*GP*G)-3')	C, F	13	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*CP*TP*TP*GP*AP*CP*CP*AP*AP*TP*A)-3')	D, E	13	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.251 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.207 (Depositor) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.555	α = 90
b = 59.555	β = 90
c = 213.367	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Li, F.D., Yang, Y., Shi, Y.Y.

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-11-20
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references