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- PDB-9b4p: Tetramer Formation of the BCL11A ZF0 Domain -

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Basic information

Entry
Database: PDB / ID: 9b4p
TitleTetramer Formation of the BCL11A ZF0 Domain
ComponentsB-cell lymphoma/leukemia 11A
KeywordsTRANSCRIPTION / Sickle cell disease / BCL11A / Tetramerization / hemoglobin / Transcription factor
Function / homology
Function and homology information


negative regulation of neuron remodeling / negative regulation of branching morphogenesis of a nerve / transcription regulatory region nucleic acid binding / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / negative regulation of dendrite development / regulation of dendrite development / negative regulation of axon extension / positive regulation of collateral sprouting ...negative regulation of neuron remodeling / negative regulation of branching morphogenesis of a nerve / transcription regulatory region nucleic acid binding / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / negative regulation of dendrite development / regulation of dendrite development / negative regulation of axon extension / positive regulation of collateral sprouting / ALK mutants bind TKIs / cellular response to L-glutamate / paraspeckles / SWI/SNF complex / protein sumoylation / transcription coregulator activity / positive regulation of neuron projection development / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / Signaling by ALK fusions and activated point mutants / negative regulation of neuron projection development / DNA-binding transcription factor binding / postsynapse / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / positive regulation of gene expression / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / BCL-11A-like CCHC zinc finger / : / C2H2 zinc finger / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
BCL11 transcription factor A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsYin, M. / Tenglin, K. / Orkin, S.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2024
Title: A tetramer of BCL11A is required for stable protein production and fetal hemoglobin silencing.
Authors: Zheng, G. / Yin, M. / Mehta, S. / Chu, I.T. / Wang, S. / AlShaye, A. / Drainville, K. / Buyanbat, A. / Bienfait, F. / Tenglin, K. / Zhu, Q. / Orkin, S.H.
History
DepositionMar 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: B-cell lymphoma/leukemia 11A
C: B-cell lymphoma/leukemia 11A
A: B-cell lymphoma/leukemia 11A
D: B-cell lymphoma/leukemia 11A
E: B-cell lymphoma/leukemia 11A
F: B-cell lymphoma/leukemia 11A
G: B-cell lymphoma/leukemia 11A
H: B-cell lymphoma/leukemia 11A
I: B-cell lymphoma/leukemia 11A
J: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,06320
Polymers32,40910
Non-polymers65410
Water32418
1
B: B-cell lymphoma/leukemia 11A
C: B-cell lymphoma/leukemia 11A
hetero molecules

B: B-cell lymphoma/leukemia 11A
C: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2258
Polymers12,9644
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPISA
2
E: B-cell lymphoma/leukemia 11A
F: B-cell lymphoma/leukemia 11A
hetero molecules

A: B-cell lymphoma/leukemia 11A
D: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2258
Polymers12,9644
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
MethodPISA
3
I: B-cell lymphoma/leukemia 11A
J: B-cell lymphoma/leukemia 11A
hetero molecules

G: B-cell lymphoma/leukemia 11A
H: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2258
Polymers12,9644
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)100.404, 58.311, 70.087
Angle α, β, γ (deg.)90.000, 134.122, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-201-

HOH

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Components

#1: Protein/peptide
B-cell lymphoma/leukemia 11A / BCL-11A / B-cell CLL/lymphoma 11A / COUP-TF-interacting protein 1 / Ecotropic viral integration ...BCL-11A / B-cell CLL/lymphoma 11A / COUP-TF-interacting protein 1 / Ecotropic viral integration site 9 protein homolog / EVI-9 / Zinc finger protein 856


Mass: 3240.883 Da / Num. of mol.: 10 / Fragment: ZF0 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL11A, CTIP1, EVI9, KIAA1809, ZNF856 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H165
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 7.3
Details: 0.2M potassium nitrate, 0.1M Tris-HCl pH 7.3, 20% PEG3350

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.558→50.31 Å / Num. obs: 31144 / % possible obs: 97.32 % / Redundancy: 3.4 % / Biso Wilson estimate: 64.5 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.1415 / Rpim(I) all: 0.09056 / Rrim(I) all: 0.1686 / Net I/σ(I): 5.28
Reflection shellResolution: 2.558→2.649 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.6798 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 955 / CC1/2: 0.637 / CC star: 0.882 / Rpim(I) all: 0.4307 / Rrim(I) all: 0.8074 / % possible all: 98.56

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→50.31 Å / SU ML: 0.5851 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 44.8783 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2941 767 4.44 %
Rwork0.278 16506 -
obs0.2789 17273 93.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.23 Å2
Refinement stepCycle: LAST / Resolution: 2.56→50.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 10 18 2252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612254
X-RAY DIFFRACTIONf_angle_d1.02273002
X-RAY DIFFRACTIONf_chiral_restr0.0491339
X-RAY DIFFRACTIONf_plane_restr0.0059379
X-RAY DIFFRACTIONf_dihedral_angle_d21.3327868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.750.40191660.4023398X-RAY DIFFRACTION95.75
2.75-3.030.41091060.37623384X-RAY DIFFRACTION94.91
3.03-3.470.46161560.37183317X-RAY DIFFRACTION94.3
3.47-4.370.3471340.2743223X-RAY DIFFRACTION90.83
4.37-50.310.22572050.21243184X-RAY DIFFRACTION91.62

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