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- PDB-6ki6: Crystal structure of BCL11A in complex with gamma-globin -115 HPF... -

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Basic information

Entry
Database: PDB / ID: 6ki6
TitleCrystal structure of BCL11A in complex with gamma-globin -115 HPFH region
Components
  • B-cell lymphoma/leukemia 11A
  • DNA (5'-D(*AP*TP*AP*TP*TP*GP*GP*TP*CP*AP*AP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*TP*TP*GP*AP*CP*CP*AP*AP*TP*A)-3')
KeywordsTRANSCRIPTION/DNA / Transcription factor / DNA binding / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


negative regulation of neuron remodeling / transcription regulatory region nucleic acid binding / negative regulation of branching morphogenesis of a nerve / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / regulation of dendrite development / negative regulation of dendrite development / negative regulation of axon extension / cellular response to L-glutamate ...negative regulation of neuron remodeling / transcription regulatory region nucleic acid binding / negative regulation of branching morphogenesis of a nerve / negative regulation of dendrite extension / negative regulation of protein homooligomerization / negative regulation of collateral sprouting / regulation of dendrite development / negative regulation of dendrite development / negative regulation of axon extension / cellular response to L-glutamate / positive regulation of collateral sprouting / paraspeckles / ALK mutants bind TKIs / SWI/SNF complex / protein sumoylation / transcription coregulator activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear matrix / positive regulation of neuron projection development / Signaling by ALK fusions and activated point mutants / negative regulation of neuron projection development / postsynapse / DNA-binding transcription factor binding / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor 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 / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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
DNA / DNA (> 10) / B-cell lymphoma/leukemia 11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLi, F.D. / Yang, Y. / Shi, Y.Y.
CitationJournal: Cell Res. / Year: 2019
Title: Structural insights into the recognition of gamma-globin gene promoter by BCL11A.
Authors: Yang, Y. / Xu, Z. / He, C. / Zhang, B. / Shi, Y. / Li, F.
History
DepositionJul 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: B-cell lymphoma/leukemia 11A
B: B-cell lymphoma/leukemia 11A
C: DNA (5'-D(*AP*TP*AP*TP*TP*GP*GP*TP*CP*AP*AP*GP*G)-3')
D: DNA (5'-D(*TP*CP*CP*TP*TP*GP*AP*CP*CP*AP*AP*TP*A)-3')
E: DNA (5'-D(*TP*CP*CP*TP*TP*GP*AP*CP*CP*AP*AP*TP*A)-3')
F: DNA (5'-D(*AP*TP*AP*TP*TP*GP*GP*TP*CP*AP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,49911
Polymers41,1726
Non-polymers3275
Water1,24369
1
A: B-cell lymphoma/leukemia 11A
C: DNA (5'-D(*AP*TP*AP*TP*TP*GP*GP*TP*CP*AP*AP*GP*G)-3')
D: DNA (5'-D(*TP*CP*CP*TP*TP*GP*AP*CP*CP*AP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7826
Polymers20,5863
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-25 kcal/mol
Surface area9510 Å2
MethodPISA
2
B: B-cell lymphoma/leukemia 11A
E: DNA (5'-D(*TP*CP*CP*TP*TP*GP*AP*CP*CP*AP*AP*TP*A)-3')
F: DNA (5'-D(*AP*TP*AP*TP*TP*GP*GP*TP*CP*AP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7175
Polymers20,5863
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-61 kcal/mol
Surface area7580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.555, 59.555, 213.367
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein B-cell lymphoma/leukemia 11A


Mass: 12644.539 Da / Num. of mol.: 2
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: DNA chain DNA (5'-D(*AP*TP*AP*TP*TP*GP*GP*TP*CP*AP*AP*GP*G)-3')


Mass: 4030.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*CP*CP*TP*TP*GP*AP*CP*CP*AP*AP*TP*A)-3')


Mass: 3910.574 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate trihydrate (pH6.5), 18% w/v polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 16230 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.03 / Rrim(I) all: 0.089 / Χ2: 0.881 / Net I/σ(I): 9.1 / Num. measured all: 141021
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.547.80.9947570.7490.3661.0620.7299.9
2.54-2.597.90.8058030.8090.2930.8590.74199.5
2.59-2.648.50.6197910.8980.2160.6570.72999.6
2.64-2.698.50.5537850.9070.1930.5870.77399.5
2.69-2.758.30.4937880.9220.1750.5250.776100
2.75-2.828.60.3958000.9690.140.420.805100
2.82-2.898.50.3088010.9730.1090.3280.8100
2.89-2.968.70.2667940.9720.0940.2820.831100
2.96-3.058.60.2098030.9770.0740.2220.887100
3.05-3.158.50.1858000.9830.0670.1970.913100
3.15-3.268.30.1327870.9920.0480.141.095100
3.26-3.398.70.1088010.9950.0390.1151.145100
3.39-3.559.40.0918370.9940.0310.0961.118100
3.55-3.739.60.0848070.9960.0290.0881.092100
3.73-3.979.70.0798210.9960.0270.0831.076100
3.97-4.279.40.0688170.9960.0240.0730.973100
4.27-4.78.50.0628130.9960.0230.0660.882100
4.7-5.3890.0588400.9970.0210.0620.792100
5.38-6.789.40.0538550.9980.0180.0560.701100
6.78-407.90.0569300.9950.0220.060.67599.6

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→37.078 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.44
RfactorNum. reflection% reflection
Rfree0.2514 744 4.7 %
Rwork0.2067 --
obs0.2088 15839 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 173.53 Å2 / Biso mean: 60.9986 Å2 / Biso min: 13.31 Å2
Refinement stepCycle: final / Resolution: 2.5→37.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1051 1054 5 69 2179
Biso mean--55.38 39.62 -
Num. residues----185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.6930.29521150.2549287496
2.693-2.96390.30151790.25852963100
2.9639-3.39250.26931370.21853003100
3.3925-4.27320.25011460.18453062100
4.2732-37.0780.21781670.18963193100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.9260.495-4.08821.8768-0.04653.73080.57941.11050.6959-0.4952-0.00050.307-0.2672-1.03310.25640.40070.1526-0.02630.2548-0.00270.3448-4.688854.6639-47.3663
25.3779-2.1617-3.3385.34480.00713.42120.1219-0.3263-0.01460.25970.01040.211-0.2714-0.1954-0.07950.1722-0.0385-0.05940.1865-0.07520.18841.255446.4783-42.8297
34.7578-3.53281.94253.1524-1.64684.58910.11970.0051-0.3768-0.43990.03720.2090.0775-0.0693-0.10280.1945-0.0058-0.05810.1229-0.05060.147615.017339.3962-42.1741
44.57621.0715-0.83976.2712-2.73611.87340.146-0.0859-0.5313-0.2852-0.319-1.06940.49050.76250.39670.25040.0786-0.04670.23820.02590.402127.879233.3053-36.6822
55.9161.5642-3.12724.8853-2.69663.53850.1581-0.53960.3630.5792-0.1761-0.7214-0.74690.90280.00660.3659-0.0488-0.12170.3122-0.08680.388926.704539.7377-29.6411
62.0112-1.08320.45793.6499-2.78742.22870.08980.30470.389-0.9354-0.48240.7889-1.3559-0.60540.19720.69550.2625-0.13080.4423-0.05970.46079.986645.6106-22.461
71.3665-0.78650.81563.9770.91981.0394-0.0364-1.1811-0.24541.09650.02050.1501-1.25511.2997-0.20180.95390.0310.04531.5175-0.13610.335615.9248.0691-3.3281
85.6289-0.75972.13421.8027-1.7563.5945-0.01410.35350.5737-0.1457-0.0948-0.27-0.21310.1549-0.10970.2687-0.00950.00080.1894-0.02180.285315.035751.4045-48.4806
94.69851.20381.51284.0721-0.5065.0097-0.01480.34830.6089-0.2003-0.0117-0.5313-0.5029-0.0380.16030.29810.0515-0.04390.2359-0.06830.401511.798850.7346-49.1629
104.6267-1.48911.21483.32080.34830.46510.1974-0.92190.26730.65680.39641.1517-1.0014-0.3378-0.42851.48140.48050.33880.82470.15350.73584.323444.8288-8.9399
112.12941.6905-1.14411.2957-0.90992.9428-0.4264-1.358-0.3160.98460.31180.7634-1.21660.05330.07831.15360.58430.13381.0340.20540.72193.273543.2977-6.5032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 740 through 753 )A740 - 753
2X-RAY DIFFRACTION2chain 'A' and (resid 754 through 770 )A754 - 770
3X-RAY DIFFRACTION3chain 'A' and (resid 771 through 792 )A771 - 792
4X-RAY DIFFRACTION4chain 'A' and (resid 793 through 811 )A793 - 811
5X-RAY DIFFRACTION5chain 'A' and (resid 812 through 824 )A812 - 824
6X-RAY DIFFRACTION6chain 'B' and (resid 742 through 765 )B742 - 765
7X-RAY DIFFRACTION7chain 'B' and (resid 766 through 793 )B766 - 793
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 13 )C1 - 13
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 13 )D1 - 13
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 13 )E1 - 13
11X-RAY DIFFRACTION11chain 'F' and (resid 1 through 13 )F1 - 13

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