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- PDB-8tlo: Crystal Structure Analysis of BCL11A in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 8tlo
TitleCrystal Structure Analysis of BCL11A in complex with DNA
Components
  • B-cell lymphoma/leukemia 11A
  • DNA (5'-D(P*CP*GP*AP*CP*CP*GP*CP*AP*TP*TP*GP*GP*TP*CP*AP*AP*GP*CP*G)-3')
  • DNA (5'-D(P*GP*CP*TP*TP*GP*AP*CP*CP*AP*AP*TP*GP*CP*GP*GP*TP*CP*GP*C)-3')
KeywordsTRANSCRIPTION / 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 / positive regulation of collateral sprouting ...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 / positive regulation of collateral sprouting / paraspeckles / cellular response to L-glutamate / ALK mutants bind TKIs / SWI/SNF complex / protein sumoylation / transcription coregulator activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of neuron projection development / nuclear matrix / Signaling by ALK fusions and activated point mutants / negative regulation of neuron projection development / DNA-binding transcription factor binding / postsynapse / protein heterodimerization activity / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 2.76 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: Structure / Year: 2024
Title: Structural insights into the DNA-binding mechanism of BCL11A: The integral role of ZnF6
Authors: 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.
History
DepositionJul 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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: DNA (5'-D(P*CP*GP*AP*CP*CP*GP*CP*AP*TP*TP*GP*GP*TP*CP*AP*AP*GP*CP*G)-3')
C: DNA (5'-D(P*GP*CP*TP*TP*GP*AP*CP*CP*AP*AP*TP*GP*CP*GP*GP*TP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6006
Polymers24,4043
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.740, 60.870, 78.350
Angle α, β, γ (deg.)90.00, 108.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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 BL21(DE3) (bacteria) / References: UniProt: Q9H165
#2: DNA chain DNA (5'-D(P*CP*GP*AP*CP*CP*GP*CP*AP*TP*TP*GP*GP*TP*CP*AP*AP*GP*CP*G)-3')


Mass: 5830.774 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*GP*CP*TP*TP*GP*AP*CP*CP*AP*AP*TP*GP*CP*GP*GP*TP*CP*GP*C)-3')


Mass: 5821.760 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
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: 5.42 Å3/Da / Density % sol: 77.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 30% PEG6K and 0.1M Na Citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.76→55.45 Å / Num. obs: 13593 / % possible obs: 99.9 % / Redundancy: 8.6 % / CC1/2: 0.99 / Net I/σ(I): 8.35
Reflection shellResolution: 2.76→2.859 Å / Redundancy: 3.6 % / Num. unique obs: 1330 / CC1/2: 0.401

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→55.45 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 51.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 658 4.9 %
Rwork0.2518 --
obs0.2529 13429 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.76→55.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms663 779 3 0 1445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.825
X-RAY DIFFRACTIONf_dihedral_angle_d32.923467
X-RAY DIFFRACTIONf_chiral_restr0.038248
X-RAY DIFFRACTIONf_plane_restr0.008151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.970.67821380.70762484X-RAY DIFFRACTION98
2.97-3.270.42511370.47452550X-RAY DIFFRACTION99
3.27-3.750.3361070.33082526X-RAY DIFFRACTION97
3.75-4.720.24291250.22612582X-RAY DIFFRACTION99
4.72-55.450.22381510.19752629X-RAY DIFFRACTION100
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)
11.6353-1.7623-0.32071.88051.61286.90850.01550.3059-0.28-0.65020.40652.38680.34510.0158-0.00031.5819-0.0195-0.0161.45980.18491.727520.5056-2.944-1.3971
23.51581.09322.69082.5856-0.00794.446-0.1666-0.31340.63030.1778-0.5295-1.392-0.38490.5795-0.00111.6996-0.07320.06181.60110.03551.14124.719619.451310.4909
34.77134.4465-0.54864.2901-0.88141.3197-0.8491.0821-2.2320.3612-0.5174-2.12682.31820.9176-0.48282.2237-0.086-0.56781.40640.12721.295836.252320.402916.1521
41.28161.1994-0.16292.12490.92241.22030.5902-2.6417-1.42563.8302-0.9214-3.37450.43821.78730.00033.7499-0.2312-0.74183.64960.48592.760732.81315.845627.0993
50.3102-0.56180.1841.8483-0.4837-0.08530.3849-0.6761-0.7858-0.1472-0.2241-0.6630.920.04460.00021.8643-0.071-0.13452.04960.27762.03189.88551.44197.6857
63.20720.4393-0.8684.5669-4.58094.40341.2766-0.6362-2.31121.3564-0.0402-0.10110.71920.54410.02022.3887-0.0245-0.3851.95630.17672.222813.61433.29829.9117
70.62920.8305-0.28651.3295-0.65950.2822-0.6567-2.1635-0.59132.2869-0.2654-0.7871-2.24320.6108-0.00233.5324-0.2648-1.04473.67430.47463.406836.47416.333830.5647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 741 through 770 )
2X-RAY DIFFRACTION2chain 'A' and (resid 771 through 811 )
3X-RAY DIFFRACTION3chain 'A' and (resid 812 through 825 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 10 )
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 19 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 10 )
7X-RAY DIFFRACTION7chain 'C' and (resid 11 through 19 )

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