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- PDB-12uq: BCL11B ZF2-3 in Complex with a DNA Sequence Containing Two Bindin... -

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Basic information

Entry
Database: PDB / ID: 12uq
TitleBCL11B ZF2-3 in Complex with a DNA Sequence Containing Two Binding Sites (Motifs TGTCCC and TGGCCT)
Components
  • B-cell lymphoma/leukemia 11B
  • Strand Bottom
  • Strand Top
KeywordsDNA BINDING PROTEIN/DNA / TRANSCRIPTION FACTOR / DNA BINDING / TRANSCRIPTION / TRANSCRIPTION-DNA COMPLEX / 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: 3.29 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: Strand Top
B: Strand Bottom
F: B-cell lymphoma/leukemia 11B
C: B-cell lymphoma/leukemia 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,84114
Polymers27,0534
Non-polymers78810
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.290, 65.854, 46.809
Angle α, β, γ (deg.)90.000, 97.209, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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DNA chain , 2 types, 2 molecules AB

#1: DNA chain Strand Top


Mass: 6077.903 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain Strand Bottom


Mass: 6194.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 1 types, 2 molecules FC

#3: 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.: 2 / 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

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Non-polymers , 5 types, 15 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-UNX / UNKNOWN LIGAND


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.54 Å3/Da / Density % sol: 65.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 26 % w/v PEG 2000 MME, 0.1 M Bis-Tris pH 5.8

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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: Feb 6, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919901 Å / Relative weight: 1
ReflectionResolution: 3.14→35.3 Å / Num. obs: 13376 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 79.83 Å2 / CC1/2: 0.988 / Net I/σ(I): 2.9
Reflection shellResolution: 3.14→3.2 Å / Num. unique obs: 636 / CC1/2: 0.768 / % 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: 3.29→35.3 Å / SU ML: 0.5223 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.9362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2954 591 5.35 %
Rwork0.2677 10466 -
obs0.2692 11057 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.84 Å2
Refinement stepCycle: LAST / Resolution: 3.29→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms847 820 32 5 1704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031822
X-RAY DIFFRACTIONf_angle_d0.48942598
X-RAY DIFFRACTIONf_dihedral_angle_d26.1043741
X-RAY DIFFRACTIONf_chiral_restr0.0281280
X-RAY DIFFRACTIONf_plane_restr0.0013189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.620.39231430.33992476X-RAY DIFFRACTION92.68
3.62-4.140.31951410.29642657X-RAY DIFFRACTION99.68
4.14-5.220.30421560.28852654X-RAY DIFFRACTION99.82
5.22-35.30.24611510.2192679X-RAY DIFFRACTION99.96
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)
13.29480.81023.15760.91472.41696.79230.66230.02861.6289-0.1889-0.53520.8805-0.1908-0.1556-1.03171.86030.2809-0.68420.7083-0.1871.6183-15.0428-87.269612.8503
20.40070.59650.00092.39890.28670.0549-0.6029-0.15840.8836-0.20190.34251.17861.98250.32240.05331.28010.2626-0.17161.0754-0.18721.1153-21.26-70.3319.1494
30.0473-0.12240.04580.3528-0.24790.30940.96110.02270.64080.4132-0.20322.57181.3581-0.67560.01361.0703-0.1012-0.09410.8426-0.03741.1414-13.9407-53.69213.1498
41.3146-0.35770.2991.73162.05162.8469-1.23330.26870.35920.3107-1.37820.2092-0.3405-1.1518-0.1491.26570.27790.00940.9395-0.01711.2997-19.7023-37.37717.297
50.4018-0.21550.25560.28130.01790.3493-0.08630.3211-0.1450.45130.0713-0.6323-0.28560.1043-0.00160.7669-0.019-0.24820.9035-0.03691.3633-16.8478-36.786514.1892
60.627-1.0537-0.15713.4204-0.28590.22461.1565-0.1960.2542-0.1017-1.4182-1.7947-0.3324-0.2363-0.16271.44510.1362-0.2950.7731-0.19741.2124-17.7834-53.39786.2821
70.30690.0250.37130.22110.09430.47140.49090.87690.1539-0.4717-0.41232.07890.155-0.4712-0.00340.69710.0155-0.04680.6053-0.09411.1526-16.8592-70.170815.5657
89.0669-9.11612.73192.0003-1.4172.77691.95362.04640.1628-0.1065-2.2998-0.622.0562-0.2924-0.23971.3692-0.0599-0.4511.03420.2171.3241-19.7245-86.19777.5015
91.7878-0.26961.23810.0406-0.1880.84980.90521.5548-0.5383-1.8673-0.5062-0.00930.8284-0.37070.18720.92590.0384-0.33050.99890.46141.0219-0.9459-40.20488.5913
100.1122-0.0607-0.01273.23621.94511.19110.535-0.34020.45560.2885-0.3392-0.87070.5121-0.29371.29230.4774-0.22490.23510.43520.16430.3995-5.7283-44.093917.2892
115.5857-3.4964.17027.1821-1.55893.33671.0295-1.2733-0.43110.52120.66751.42941.5945-0.38211.77150.7390.10530.30390.8533-0.01560.5182-14.8057-53.101127.3123
120.09810.2844-0.23860.9676-0.61820.57890.54470.5266-0.31061.4771-0.8472-0.0169-1.564-0.62360.01190.6952-0.0558-0.17510.7819-0.17711.0102-20.3249-51.600721.2739
130.0938-0.0750.11370.0595-0.09050.2243-1.99441.64730.1844-0.39-0.95771.67950.3148-0.0383-0.02291.274-0.38860.10961.0823-0.33861.1464-31.3991-57.928727.8522
144.2931-1.19040.73031.64560.45120.450.1483-0.7342-0.69380.2792-0.4322-0.41991.1075-0.8489-0.37631.1326-0.56490.08330.5427-0.08330.9043-16.7918-80.520427.6009
150.2961-0.1362-0.94470.80890.582.9874-0.3494-0.3081-0.12690.56480.69250.37410.89670.09520.9210.51480.13710.41490.49710.20790.0054-9.131-76.495121.4086
161.28880.51490.39280.8211-0.49180.7945-0.43530.2149-0.42910.08220.11280.06740.260.3096-0.20870.32860.05530.39620.68070.00130.0101-1.9831-68.166210.8983
174.7643-0.4815-0.41530.69310.27770.71340.49480.76160.9987-0.4482-0.1431-0.5915-0.14280.0288-0.52690.43970.70040.13050.6301-0.030.4587-6.8728-66.80724.0961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 5 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 6 THROUGH 10 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 11 THROUGH 15 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 16 THROUGH 20 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 1 THROUGH 5 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 6 THROUGH 10 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 11 THROUGH 15 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 16 THROUGH 20 )
9X-RAY DIFFRACTION9CHAIN 'F' AND (RESID 427 THROUGH 438 )
10X-RAY DIFFRACTION10CHAIN 'F' AND (RESID 439 THROUGH 455 )
11X-RAY DIFFRACTION11CHAIN 'F' AND (RESID 456 THROUGH 465 )
12X-RAY DIFFRACTION12CHAIN 'F' AND (RESID 466 THROUGH 477 )
13X-RAY DIFFRACTION13CHAIN 'F' AND (RESID 478 THROUGH 482 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 427 THROUGH 438 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 439 THROUGH 455 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 456 THROUGH 466 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 467 THROUGH 480 )

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