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- PDB-12un: BCL11B ZF2-3 in Complex with a DNA Sequence Observed in the Human... -

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Basic information

Entry
Database: PDB / ID: 12un
TitleBCL11B ZF2-3 in Complex with a DNA Sequence Observed in the Human Globin Locus Containing Motif TGGCCA (Oligo 4-3)-P212121 Form
Components
  • B-cell lymphoma/leukemia 11B
  • DNA Strand (Self-Annealing)
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


lymphoid lineage cell migration into thymus / hematopoietic stem cell migration / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / SWI/SNF complex / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron projection / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity ...lymphoid lineage cell migration into thymus / hematopoietic stem cell migration / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / SWI/SNF complex / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron projection / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
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) / B-cell lymphoma/leukemia 11B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsHorton, J.R. / Cheng, X. / Zhou, J. / Lee, J.
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: Biorxiv / Year: 2026
Title: Bipartite DNA binding domain of transcription factor BCL11B binds clustered short DNA sequence motifs.
Authors: Lee, J. / Zhou, J. / Horton, J.R. / Yu, M. / Muoghalu, M.D. / Khan, F.A. / Zhang, X. / Huang, Y. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionApr 19, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B-cell lymphoma/leukemia 11B
D: B-cell lymphoma/leukemia 11B
M: B-cell lymphoma/leukemia 11B
G: DNA Strand (Self-Annealing)
H: DNA Strand (Self-Annealing)
K: DNA Strand (Self-Annealing)
L: DNA Strand (Self-Annealing)
I: DNA Strand (Self-Annealing)
J: DNA Strand (Self-Annealing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,50815
Polymers46,1169
Non-polymers3926
Water905
1
A: B-cell lymphoma/leukemia 11B
I: DNA Strand (Self-Annealing)
J: DNA Strand (Self-Annealing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5035
Polymers15,3723
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: B-cell lymphoma/leukemia 11B
G: DNA Strand (Self-Annealing)
H: DNA Strand (Self-Annealing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5035
Polymers15,3723
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
M: B-cell lymphoma/leukemia 11B
K: DNA Strand (Self-Annealing)
L: DNA Strand (Self-Annealing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5035
Polymers15,3723
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.444, 49.026, 234.564
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein B-cell lymphoma/leukemia 11B / BCL-11B / B-cell CLL/lymphoma 11B / COUP-TF-interacting protein 2 / Radiation-induced tumor ...BCL-11B / B-cell CLL/lymphoma 11B / COUP-TF-interacting protein 2 / Radiation-induced tumor suppressor gene 1 protein / hRit1


Mass: 7390.648 Da / Num. of mol.: 3 / Fragment: domains ZF2-3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL11B, CTIP2, RIT1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold Plus / References: UniProt: Q9C0K0
#2: DNA chain
DNA Strand (Self-Annealing)


Mass: 3990.622 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 45% v/v Polypropylene glycol P 400, 0.1 M BIS-TRIS pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.919901 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 19, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919901 Å / Relative weight: 1
ReflectionResolution: 3.03→33.9 Å / Num. obs: 21664 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 81.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.052 / Net I/σ(I): 9.9
Reflection shellResolution: 3.03→3.08 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1026 / CC1/2: 0.503 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX2.0_5885refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.03→33.89 Å / SU ML: 0.3695 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5931
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 1008 5.2 %
Rwork0.224 18376 -
obs0.2253 19384 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.79 Å2
Refinement stepCycle: LAST / Resolution: 3.03→33.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 1590 6 5 2904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523153
X-RAY DIFFRACTIONf_angle_d0.69864545
X-RAY DIFFRACTIONf_chiral_restr0.0369490
X-RAY DIFFRACTIONf_plane_restr0.0039303
X-RAY DIFFRACTIONf_dihedral_angle_d25.87951350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.03-3.190.37711510.36542588X-RAY DIFFRACTION98.28
3.19-3.390.36371120.30692512X-RAY DIFFRACTION94.32
3.39-3.650.33561380.28152614X-RAY DIFFRACTION98.71
3.65-4.020.27211360.242698X-RAY DIFFRACTION99.58
4.02-4.60.23841570.222650X-RAY DIFFRACTION99.93
4.6-5.780.20461850.20742629X-RAY DIFFRACTION100
5.79-33.890.20331290.16982685X-RAY DIFFRACTION99.82
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)
16.77013302398575.12034762372252.54763755018972.0158447855206-3.37569717493366.12271988340.113702809386880.406860763299842.3501211536685-0.137387318411790.665575079183692.3508809977462-0.89349453714374-0.51425315733339-0.545128287589830.763220499378910.254696256981350.0981829065975650.795856715295620.240437464852350.99683747661207-32.74442396651-1.365151325707311.986012260705
25.81011132735631.0420573241057-3.00808148887685.0442614289976-3.8388640555824.93039654432050.44621083868231.09562447629790.32485792098914-0.187473882429320.083601810194345-0.182958724786030.26240396306572-0.78847890094936-0.548215545014930.951408183299820.20180357295536-0.108373472984560.800360813836270.0513380895186980.36940290965448-27.998780764209-6.735117729639814.380379690895
36.99879316387683.6413279228012-0.486947666285447.11779861245830.837573474653692.49825780874480.31810809318574-0.082171626993549-0.32645943860981-0.17694106375406-0.58074458124014-0.47857821896511-0.069480737610808-0.387409961079540.398732444240470.684099262997340.125552701572210.0456944872109680.73425356603240.111671313700230.25552723787214-17.380482416767-15.71353629116821.504508690034
43.4280222662802-3.08967871566870.195084253482852.0837317912821-4.08383948773556.2255479757732-0.30460988176398-1.25809346349690.163204285157910.88034369502453-0.078605267591736-1.1803912614073-0.632808908909071.0339127304140.270596043000790.889427063063190.30411580138578-0.0840163519561191.3938037923857-0.0903118899138720.3241342436721-8.9763309978942-10.28597146018825.785754423279
56.8961467013744-0.3801753408072-0.793250941855022.9467850742486-0.19999823921975.96012841031590.20839718597969-1.0999873449550.767593113722280.625082546040590.062751906864039-0.2024134595426-1.20760870552061.3057293193282-0.290679006246170.99012026001121-0.30726320532651-0.119283273513880.89369885679484-0.0144085292915460.46197496612224-1.75263819786750.51430808969199-9.2033895015103
69.2007679209204-1.94985284895291.31193936242615.36176283152391.90776219173796.82828384413420.367324208299980.940930779882130.232522504104020.71323659872258-0.322889259156830.59180737485731-0.11217252456407-0.0720372684641290.0379553100859320.70139173607352-0.161358864684780.14967126101870.70885042877290.196405179754610.3963319991078-19.139612233147-3.9325163828276-22.4384252744
7-0.0057750999003827-0.0047401897492171-0.023805961844309-0.0018147408107688-0.0087396810327754-0.00197152744332280.75059482258215-0.588248585074351.0611704264823-0.398323341233620.036777614913468-0.80771510768318-0.46511447512658-0.80399352049463-0.842592294103311.08182024811240.213980382234060.445342216070921.4091913931418-0.0324083322660411.5107982042599-5.437539921913923.004527612771-69.292485901946
86.84465112743541.54170508538614.35949556878582.0081741543659-2.48162504796849.7138178503040.286849558762910.51981083613050.73632997206882-1.25334312699871.6715582602117-0.89057343819353-0.272059977129111.3080941310624-2.02687098713691.05283182185840.0568231401523770.364448082931451.1938844998707-0.0390067208974190.80705176689592-12.20289342353920.323088424287-66.404090272838
92.03619508560798.3014247236388-8.38785451483318.9412416681399-7.84900895140112.07439288609610.0322247232309761.2254120659721-0.39839315819778-0.035597183124547-0.15255737666401-0.183691768976710.12333741589394-0.962982134171520.228027263418611.15504171299790.0212847633237440.197669121964071.17892985151320.150790475183280.95889944997919-24.32797833721214.718676121037-58.783252137083
101.9722033527825-4.0038451279965.61701438255357.6095325937056-0.743234617441184.47661158082680.914969989101450.0047121450376894-0.958254015163071.2284204417485-0.556706066177830.53073889390239-1.35480850562120.47774913312873-0.204732209897041.3794042637145-0.157198000677330.065853426328241.1255951981790.0261510420600960.55831385932643-22.6222782961985.4130025804395-52.277424967089
113.77390327639290.46586516901152-0.198964438442394.1053200017487-0.395526507592610.102926545411990.70607438270766-0.152666616334920.0622580480812860.839940924843520.480832840561530.72802401406918-2.0457592670441-1.2403803700506-0.699714761226611.8846475244833-0.152367306508580.115355637375931.3832843160280.207616526095790.14690726713688-15.7226854088927.2087778713914-15.698113985456
122.74858575327451.14145877225153.26413989059642.29917410605740.916168829842699.2354773646089-0.473416819837190.079827263180544-0.00651849534218520.626540917313080.368018198913540.071690884129934-0.441213820409780.311805470775220.238736825318781.40059512360010.0845150279886060.191597165205211.15381856170040.187398335613310.54237786736205-13.8341837816346.6323219069603-17.97918504918
132.5827638854142-1.3097175269038-3.516531952672.2436536445876-0.496697965299067.53629242742980.14125847881109-0.432045066703210.0085661481146959-0.48663951840050.34533798925122-0.28402285201550.782164687506371.0920269632828-0.511862796431861.73225665206680.137438713484540.20665329139842.0789121590149-0.0568232894477490.63088301517584-10.3305469462948.2316217564504-56.926177496321
142.74458504269391.2234340731685-0.726511590776562.38866519334190.75907933056276.94559647973961.00291680145760.10762135023540.133098089451780.233500155013380.086968033057188-0.0678079875453880.301723685775070.13676856160717-0.965558881631661.71441897467570.0279823382274670.02853558305061.8777266579137-0.00819348501096750.5751062680672-10.87642328931710.380904758822-54.473307510838
152.98704001158280.30117478483648-1.69717740771643.8992643040149-1.66253155350274.95490384238440.24476645516536-0.454305270022820.111082409519310.27643567970812-0.069583798915592-0.48563549013053-1.77788824884281.521159163134-0.14184432219711.5212876809034-0.1212118875888-0.027888636240191.34237924320650.00304857720946190.47970636324494-16.236492720871-0.2244793032685721.556875058318
162.2668884123230.36263085718906-0.64144721819093.3244905704675-1.83739533560646.4536960613211-0.27867886478269-0.99257169973205-0.06350654843361-0.0983226666204280.60018466050942-0.059659555540970.0702489863668981.187672910336-0.42872496100751.42578282955510.0389229179986560.0568668440933231.49584145485040.0270598669001140.4882166212674-18.067582545923-1.47699566233423.750867041501
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 427 through 438 )AA427 - 4381 - 12
22chain 'A' and (resid 439 through 450 )AA439 - 45013 - 24
33chain 'A' and (resid 451 through 466 )AA451 - 46625 - 40
44chain 'A' and (resid 467 through 480 )AA467 - 48041 - 54
55chain 'D' and (resid 427 through 450 )DF427 - 4501 - 24
66chain 'D' and (resid 451 through 481 )DF451 - 48125 - 55
77chain 'M' and (resid 427 through 438 )MG427 - 4381 - 12
88chain 'M' and (resid 439 through 450 )MG439 - 45013 - 24
99chain 'M' and (resid 451 through 466 )MG451 - 46625 - 40
1010chain 'M' and (resid 467 through 481 )MG467 - 48141 - 55
1111chain 'G' and (resid 1 through 13 )GJ1 - 13
1212chain 'H' and (resid 1 through 13 )HK1 - 13
1313chain 'K' and (resid 1 through 13 )KL1 - 13
1414chain 'L' and (resid 1 through 13 )LM1 - 13
1515chain 'I' and (resid 1 through 13 )IN1 - 13
1616chain 'J' and (resid 1 through 13 )JO1 - 13

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