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- PDB-6u9q: Crystal Structure Analysis of DNA-BCL11A Znf domain complex -

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Basic information

Entry
Database: PDB / ID: 6u9q
TitleCrystal Structure Analysis of DNA-BCL11A Znf domain complex
Components
  • B-cell lymphoma/leukemia 11A
  • DNA3
  • DNA5
KeywordsTRANSCRIPTION/DNA / Transcription factor / DNA-binding / Zn finger / 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
PHOSPHATE ION / DNA / DNA (> 10) / B-cell lymphoma/leukemia 11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.83 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of TAF1 Bromodomain
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionSep 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: B-cell lymphoma/leukemia 11A
B: DNA5
C: DNA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1059
Polymers20,6953
Non-polymers4106
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-49 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.000, 60.160, 75.790
Angle α, β, γ (deg.)90.000, 129.730, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-1309-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 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: 12751.690 Da / Num. of mol.: 1
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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA5


Mass: 3991.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA3


Mass: 3951.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 115 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: NaMalate~8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.83→47.563 Å / Num. obs: 30114 / % possible obs: 97.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 41.746 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.048 / Net I/σ(I): 15.8
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1 / Num. measured all: 5071 / Num. unique obs: 1498 / Rpim(I) all: 0.67 / Rrim(I) all: 1.25 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
XDSdata reduction
Aimless0.5.23data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→47.563 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.31
RfactorNum. reflection% reflection
Rfree0.1946 1424 4.73 %
Rwork0.1747 --
obs0.1756 30107 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.42 Å2 / Biso mean: 52.4378 Å2 / Biso min: 30.09 Å2
Refinement stepCycle: final / Resolution: 1.83→47.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms694 512 14 109 1329
Biso mean--72.15 51.43 -
Num. residues----115
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8301-1.89550.35721550.3428286798
1.8955-1.97140.31191560.2948284798
1.9714-2.06110.28571410.2554288998
2.0611-2.16980.22741680.2103285299
2.1698-2.30570.23431390.1986291299
2.3057-2.48370.24621270.1909285697
2.4837-2.73370.20321260.207291898
2.7337-3.12920.2251370.1953284596
3.1292-3.94210.15931210.1646279994
3.9421-47.5630.16811540.1369289896
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)
11.08680.60950.36281.80781.0820.64170.0283-0.29560.09850.29060.03240.4106-0.2652-0.2627-0.00180.49780.04730.04970.5777-0.00610.512414.810554.843815.2525
21.84810.3567-1.01661.7099-0.38571.6157-0.1802-0.3062-0.03030.19660.12180.5225-0.5427-0.5043-0.00130.51580.0395-0.00890.5302-0.03680.641713.92655.283612.0533
33.36790.493-1.55391.8842-1.94152.46160.0299-0.13840.40610.37430.06270.0232-0.66020.21250.00080.5819-0.0052-0.02060.44490.00420.461127.829363.34469.638
42.0822-0.77441.16012.55141.69662.91180.0675-0.2869-0.53160.4694-0.03270.08090.2584-0.35860.00030.40340.010.03640.43130.03580.445816.153241.35226.6023
50.7038-0.0789-0.21491.10140.54960.46750.26670.9501-0.1148-0.9035-0.15420.7149-0.178-1.2347-0.00130.51360.0929-0.08310.68080.0070.59219.98436.9577-4.0976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 13 )B1 - 13
2X-RAY DIFFRACTION2chain 'C' and (resid 1 through 13 )C1 - 13
3X-RAY DIFFRACTION3chain 'A' and (resid 737 through 770 )A737 - 770
4X-RAY DIFFRACTION4chain 'A' and (resid 771 through 802 )A771 - 802
5X-RAY DIFFRACTION5chain 'A' and (resid 803 through 825 )A803 - 825

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