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- PDB-9e6r: BCL11A ZF4-6 in Complex with a DNA Sequence Observed in the Human... -

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Basic information

Entry
Database: PDB / ID: 9e6r
TitleBCL11A ZF4-6 in Complex with a DNA Sequence Observed in the Human Globin Locus Containing Motif TGACCA
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 / 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
DNA / DNA (> 10) / BCL11 transcription factor A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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
CitationJournal: 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.
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: DNA Strand I
C: DNA Strand II
D: B-cell lymphoma/leukemia 11A
Y: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,19819
Polymers49,3785
Non-polymers82014
Water2,792155
1
A: B-cell lymphoma/leukemia 11A
B: DNA Strand I
C: DNA Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,93012
Polymers24,4333
Non-polymers4969
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6654
Polymers12,4721
Non-polymers1933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
Y: B-cell lymphoma/leukemia 11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6033
Polymers12,4721
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.328, 61.328, 244.410
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

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Components

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Protein , 1 types, 3 molecules ADY

#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.: 3 / 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 BC

#2: DNA chain DNA Strand I


Mass: 6197.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA Strand II


Mass: 5763.761 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 169 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 24 % v/v Ethanol, 0.1 M HEPES 7.8, 40 mM Magnesium chloride hexahydrate

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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: Apr 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.09→33.93 Å / Num. obs: 52590 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 46.51 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.048 / Net I/σ(I): 9.8
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2838 / CC1/2: 0.35 / Rpim(I) all: 0.964 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→33.93 Å / SU ML: 0.2708 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.7942
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2383 2591 4.93 %
Rwork0.2043 49999 -
obs0.2059 52590 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.89 Å2
Refinement stepCycle: LAST / Resolution: 2.09→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1539 777 26 155 2497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522464
X-RAY DIFFRACTIONf_angle_d0.7393472
X-RAY DIFFRACTIONf_chiral_restr0.0425374
X-RAY DIFFRACTIONf_plane_restr0.0058304
X-RAY DIFFRACTIONf_dihedral_angle_d22.35771010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.130.3551440.33282597X-RAY DIFFRACTION98.53
2.13-2.170.29351390.32222633X-RAY DIFFRACTION99.14
2.17-2.210.35541520.31842600X-RAY DIFFRACTION99.64
2.21-2.260.31151460.2982626X-RAY DIFFRACTION99.93
2.26-2.310.33191470.29582607X-RAY DIFFRACTION99.96
2.31-2.370.29351440.28242649X-RAY DIFFRACTION100
2.37-2.440.28941230.27032648X-RAY DIFFRACTION100
2.44-2.510.29491510.252598X-RAY DIFFRACTION100
2.51-2.590.25011550.24272648X-RAY DIFFRACTION100
2.59-2.680.28121370.22582644X-RAY DIFFRACTION100
2.68-2.790.28921180.23792691X-RAY DIFFRACTION99.93
2.79-2.910.30291210.23272655X-RAY DIFFRACTION99.96
2.91-3.070.29981160.23622636X-RAY DIFFRACTION99.96
3.07-3.260.24281550.2192597X-RAY DIFFRACTION99.24
3.26-3.510.20741130.19312628X-RAY DIFFRACTION98.46
3.51-3.860.23011080.1822640X-RAY DIFFRACTION99.85
3.86-4.420.20741480.14932647X-RAY DIFFRACTION99.93
4.42-5.570.1621370.16722640X-RAY DIFFRACTION99.96
5.57-33.930.21971370.17812615X-RAY DIFFRACTION99.39
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)
14.762498300173.96068648779-1.419846086955.218367793570.271547388382.27663222124-0.1263625505060.562449167439-0.63094007427-0.2351133317850.4863947201620.3521738495980.212718959431-0.222674341217-0.3843878003330.332918320968-0.05594583206330.002976018807530.5269578678-0.005439596581820.45610849448420.6630653558-8.1265588890337.7464932564
22.40957485308-1.275939742442.35967040684.24558241134-5.186851950176.825852400620.175382606861-0.03064236762530.1937215214290.57183581487-0.05779534049310.751413033851-0.518444250053-0.42697469637-0.09221912959960.3480009293040.03253217967670.01062718119260.389248537625-0.02876957212120.37338940047224.35510134068.7365542566529.8251044322
33.69842893122-1.595274814543.82430705654.76761422566-3.439676652384.77854162433-0.01865158257240.334546619540.721264865583-0.176326247441-0.241194183001-0.579811321517-0.4242043726540.9459534334250.2530871941360.4309739356810.04142311539770.02106730334020.5537457595890.006023252166370.48622242751728.416434325720.073817049120.9429977007
47.74832825864-1.08453966976-0.1673650505853.225705960722.490014792834.70940515190.4638743214031.00055187682-0.269399743768-0.756381547822-0.4388336205960.67465736319-0.11393415037-0.470125314058-0.08727303667690.4265822877920.0423596317728-0.06004071662670.529501085643-0.02497319937470.4294608620622.466336013315.620982621514.9939774256
52.16575895893-3.277517889483.406355149535.01398331059-5.106229491255.337792998150.393835004679-0.978708487771-0.3181811884851.902692324880.4541214210170.895492328963-0.976798993076-0.41934675755-0.7709400378790.682035091938-0.07016737340880.06508209812030.7494542779050.09090806048370.40002682391325.3891534115-3.24167231874-4.86264527702
61.84531080143-0.221073710689-0.04812322410333.14940765122-1.755546881512.839023470830.2742660135690.0587257487997-0.237289414231-0.5405239858250.1220710305610.2676460203880.4031322337120.135859101812-0.3446557520350.364721023894-0.0108640766913-0.04109749905570.427094389071-0.08916357390710.32631154156332.5948707305-1.6718811309125.8304224785
78.81379714148-1.26354532368-1.694019305017.664475504682.911023369614.71370750898-0.102877162288-0.206873550584-0.20867086763-0.67540519551-0.1361658291370.301815567186-0.5787094350210.6969362644990.2625021876060.2972697908140.0190226742024-0.04042573764020.3052056149330.02406590289910.29809832773932.6030862942-1.6114639152833.006092371
87.45586467048-2.00878931598-2.089360787077.907627730556.382753584728.647501265890.4483621716620.01107464054970.00669493825049-1.208939503890.302367312174-0.0554049955642-1.755877071210.590362875278-0.7019347739540.613528752147-0.074983680953-0.1025095855850.6426842241930.02055245908390.34482645488130.14151909460.2283510754973.86886088189
97.729367337291.359636539671.003271298728.004173295745.249455038683.81632645698-0.609444910946-0.3770472998061.169648767980.587683192030.385952094064-0.486875855812-0.5132447968421.06206386510.2471647431140.4947240625520.132862026967-0.1233129144820.684749798334-0.0535128005540.65780906898147.8042936774-8.1229471392847.293584244
105.590749336020.2003986039342.846616832539.743492772253.099590735525.999574154290.0513095324149-0.970316668042-0.4271439253980.34065168264-0.223958572430.7047366918010.422986654472-0.8242225161130.1563079097210.3467270059150.04028286655030.04143175343950.5384284364370.07161078737750.40324048704838.3302081316-15.658180380443.5782433372
115.40044821652-3.09936311734-1.502934115152.94490196193-0.05684788279037.798556060680.195984988740.610558256413-0.156102004611-0.68953955108-0.436712499644-0.5408800174620.7106437873681.000662545020.2798514688950.4584761952210.1653899445320.05580163654580.511262009139-0.001272545038530.42133251797444.9273039148-15.582566944330.3470102952
128.873342072562.7131932730.292388484627.31831769067-3.574895443085.38408347205-0.06400550021190.992825142405-1.01693025388-1.074501952180.0935054546627-0.6271161946730.8127771406730.584611606713-0.06881469634220.611476902916-0.0569137202080.01170250149590.7216337454-0.1726775823280.53640426359546.32217986255.453880815788.4587874925
137.58320607664-4.164670799953.407479971352.57874422301-2.610033784533.38766064423-1.06866859204-0.04918165994481.735062659790.214801994962-0.135916253749-0.355290617021-1.41277056146-0.4407649089550.6174811485251.491573009370.0954911497755-0.579926482250.8609612550.3808563562771.2842610630937.76251701924.9760131508-0.946521503764
141.33652154264-1.76244590674-0.7705744074523.47388952054-1.1093612184.39845817458-0.7632073110890.4697309536971.30137263391-1.01809489449-0.9688782913611.65953139596-1.43327515602-0.4544433618151.581504846291.08679272533-0.154219002765-0.6233989132890.990257336151-0.01289949169531.2781296761634.329121681518.31959345862.39124553019
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 741 through 770 )AA741 - 7701 - 30
22chain 'A' and (resid 771 through 791 )AA771 - 79131 - 51
33chain 'A' and (resid 792 through 806 )AA792 - 80652 - 66
44chain 'A' and (resid 807 through 825 )AA807 - 82567 - 85
55chain 'B' and (resid 1 through 5 )BJ1 - 5
66chain 'B' and (resid 6 through 20 )BJ6 - 20
77chain 'C' and (resid 1 through 10 )CK1 - 10
88chain 'C' and (resid 11 through 19 )CK11 - 19
99chain 'D' and (resid 767 through 781 )DL767 - 7811 - 15
1010chain 'D' and (resid 782 through 801 )DL782 - 80116 - 35
1111chain 'D' and (resid 802 through 825 )DL802 - 82536 - 59
1212chain 'Y' and (resid 742 through 770 )YM742 - 7701 - 29
1313chain 'Y' and (resid 771 through 775 )YM771 - 77530 - 34
1414chain 'Y' and (resid 776 through 792 )YM776 - 79235 - 51

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