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- PDB-9e6t: BCL11A ZF4-6 in Complex with a DNA Sequence Observed in the Human... -

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Basic information

Entry
Database: PDB / ID: 9e6t
TitleBCL11A ZF4-6 in Complex with a DNA Sequence Observed in the Human Globin Locus Containing Motif TGCCCA
Components
  • B-cell lymphoma/leukemia 11A
  • DNA Strand I
  • DNA Strand II
KeywordsDNA BINDING PROTEIN/DNA / TRANSCRIPTION FACTOR / DNA BINDING / TRANSCRIPTION / TRANSCRIPTION-DNA COMPLEX / GLOBIN LOCUS / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / regulation of dendrite development / negative 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 / regulation of dendrite development / negative regulation of dendrite development / negative regulation of axon extension / positive regulation of collateral sprouting / cellular response to L-glutamate / ALK mutants bind TKIs / 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 / protein heterodimerization activity / 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 / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / : / 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
DNA / DNA (> 10) / B-cell lymphoma/leukemia 11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.78 Å
AuthorsHorton, J.R. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134744 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
Citation
Journal: Nat Commun / Year: 2025
Title: Multimeric transcription factor BCL11A utilizes two zinc-finger tandem arrays to bind clustered short sequence motifs.
Authors: Horton, J.R. / Yu, M. / Zhou, J. / Tran, M. / Anakal, R.R. / Lu, Y. / Blumenthal, R.M. / Zhang, X. / Huang, Y. / Zhang, X. / Cheng, X.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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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: B-cell lymphoma/leukemia 11A
I: DNA Strand I
J: DNA Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,38211
Polymers36,9274
Non-polymers4557
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer, expected 1:1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.230, 59.230, 247.124
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1005-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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: 12472.312 Da / Num. of mol.: 2 / Fragment: Zinc finger domains 4-6
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) / Variant (production host): GoldPlus / References: UniProt: Q9H165

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DNA chain , 2 types, 2 molecules IJ

#2: DNA chain DNA Strand I


Mass: 5615.642 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA Strand II


Mass: 6367.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 26 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15 % w/v PEG 1000, 30 % v/v PEG 300, 0.1 M Bis-Tris Propane 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.78→33.82 Å / Num. obs: 20789 / % possible obs: 100 % / Redundancy: 25.8 % / Biso Wilson estimate: 67.51 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.065 / Net I/σ(I): 10.7
Reflection shellResolution: 2.78→2.82 Å / Redundancy: 27.3 % / Num. unique obs: 1057 / CC1/2: 0.429 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.78→33.82 Å / SU ML: 0.4619 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.68
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2806 1055 5.07 %
Rwork0.2462 19734 -
obs0.2479 20789 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.91 Å2
Refinement stepCycle: LAST / Resolution: 2.78→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 784 10 19 2083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292194
X-RAY DIFFRACTIONf_angle_d0.49053128
X-RAY DIFFRACTIONf_chiral_restr0.0341345
X-RAY DIFFRACTIONf_plane_restr0.002263
X-RAY DIFFRACTIONf_dihedral_angle_d23.5441860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.90.36841330.39482360X-RAY DIFFRACTION93.93
2.9-3.050.37591660.35582480X-RAY DIFFRACTION99.7
3.05-3.250.39871250.35282428X-RAY DIFFRACTION96.09
3.25-3.490.33411320.29712409X-RAY DIFFRACTION95.03
3.5-3.850.291430.27372451X-RAY DIFFRACTION98.93
3.85-4.40.24761050.21582555X-RAY DIFFRACTION99.63
4.4-5.540.2471290.21152522X-RAY DIFFRACTION99.7
5.55-33.820.22531220.18442529X-RAY DIFFRACTION99.85
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)
13.07645468716-3.437411999732.875483187837.572922594361.674275895819.48172219680.7131170085291.155552769790.996419498447-0.785502201371-0.297519701973-2.04235409145-0.2988618353981.40475656301-0.06415600843920.968696440274-0.1711271273330.3736395680041.79854296032-0.0443084820780.95121490123316.287937263726.284473023714.1192009221
25.590443609463.280979759723.039511415915.461219027943.408914248799.1971812723-0.157672420762-0.257102961268-0.659626315257-1.449647348430.34906105533-0.302448889815-0.7061505963770.440661910742-0.187990629641.084880538670.1691608712150.09539991513070.921364796637-0.2342831687050.6995792172294.8421055296316.458780092510.0193384049
37.908579581066.149440316566.884914191364.753188185975.676871367398.00894240553-0.2906616771480.704173069351.75437272172-0.743806545056-0.6536435633431.884693484450.716992040657-1.060307556930.9136701509291.21979120178-0.0251815736337-0.2057054636421.19977597156-0.2506102424940.756460187954-9.7161246606717.44665360496.0963890378
44.600573485464.752773278150.9080782150347.468720517380.6836314331917.966723507780.5040325957591.0934465835-0.7004347551160.597193302354-0.676696161365-0.176966604639-0.286419628068-0.7488050660740.1226476732011.16842800901-0.220068339273-0.0912488563210.909854431781-0.3832804233190.850353871339-10.9645167988.9470178744-7.00117213947
57.704726308492.460308199821.751701256624.01069217973-3.213743672425.710165671910.07750508146810.0722914352486-0.1540527322350.4972571416360.195481529174-0.1514900638490.4308819197360.767577437067-0.3874824774280.689364659360.09433337873350.03963589579260.374490263074-0.06826024530750.506387080971-8.222325618516.52485905939.0414120532
63.017137745692.528276722310.4431203779476.56521119294-3.286630858615.214960143570.609027932629-0.2056381748870.5108422972960.489618060246-0.2109647741910.411723220491-0.2234080173220.938933344259-0.3403858574620.601293760267-0.0466713249660.1404492865530.440885927445-0.1592155409810.352197459465-7.3569746114933.975531630330.7383766219
78.65908751327-5.61517753649-0.6515741264454.66330086216-2.271278492692.032891649640.815457987119-0.3245220040940.677474784984-0.265674644184-0.744245389101-1.97433930889-0.7049839084711.78598076202-0.4107439620710.9896272956-0.380008772558-0.0611979277850.920798251056-0.06181682132410.7674820872441.2570794363647.130469800422.1968133553
86.72705521051-3.08309833997-0.09949841397126.732221939375.153497276825.160862649910.02419236019461.64548906594-0.752714483110.277798619095-0.2639996415010.6073673198550.7484888059260.07046476791070.0831055090480.899743266961-0.0938742469580.2105183233020.7463446978290.07275488285810.404877346166-8.5950778097143.157190981915.7438075781
94.978159041347.034192356122.797297782452.051662350334.020864480031.560728996710.933383199153-0.242123486577-1.748220424250.785194388981-0.88637178172-1.20489951209-0.25841053225-0.202622802403-0.4071678899840.9648119030060.2020130078140.1090828610611.3123035554-0.09024864060930.3526566687821.3267399574327.725857769142.6068052392
108.12358551783.901674187135.590618977647.489545916977.494496048287.983964176390.8388603763020.3978682088870.3463058711520.353199815998-0.3700629059850.03811670195030.8694770512691.73783037273-0.501458666421.285954249560.009541453001130.08141134247541.01543647583-0.1800436859570.4416669311674.796350054822.404529652125.1271602157
113.20237024518-1.32625659278-1.774162980652.455828274630.4370652893931.413666907290.291899847750.901848779502-0.2597350135-0.5714950903150.714464600074-0.2657751627610.3093627244851.03446853905-0.5676231169261.23518158850.1071176670450.09777516871961.41227231158-0.3001593189080.44706945171-1.4412201219627.87544304323.73559828446
123.576028567433.921550591752.823150500866.304952466184.996674929343.78571700062-0.2703891601730.9839051744760.683978495424-0.008055128792230.3334367529780.2303963024120.8245896262450.581618677815-0.1598613301411.4428388605-0.0008966917372080.05441547374141.38155482123-0.1457472553890.492698115717-1.333260058826.05398628522.46205960861
135.91522946985-2.51854214510.2030776580776.08742388609-2.687669604251.209880307190.326800875289-0.820084254599-0.0709702987873-0.0961792055661-0.154290335545-0.335412624561-0.2341875696290.763228621501-0.03881700610790.9342873426090.02750884452180.03730776612550.949759791243-0.07071171924040.4324242840732.3917632259224.213241723334.2896016485
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 742 through 753 )AA742 - 7531 - 12
22chain 'A' and (resid 754 through 781 )AA754 - 78113 - 40
33chain 'A' and (resid 782 through 797 )AA782 - 79741 - 56
44chain 'A' and (resid 798 through 827 )AA798 - 82757 - 86
55chain 'B' and (resid 742 through 765 )BB742 - 7651 - 24
66chain 'B' and (resid 766 through 792 )BB766 - 79225 - 51
77chain 'B' and (resid 793 through 802 )BB793 - 80252 - 61
88chain 'B' and (resid 803 through 825 )BB803 - 82562 - 84
99chain 'I' and (resid 1 through 5 )IC1 - 5
1010chain 'I' and (resid 6 through 10 )IC6 - 10
1111chain 'I' and (resid 11 through 19 )IC11 - 19
1212chain 'J' and (resid 1 through 10 )JD1 - 10
1313chain 'J' and (resid 11 through 20 )JD11 - 20

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