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

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Basic information

Entry
Database: PDB / ID: 12um
TitleBCL11B ZF2-3 in Complex with a DNA Sequence Observed in the Human Globin Locus Containing Motif TGTCCA (Oligo 3-5)
Components
  • B-cell lymphoma/leukemia 11B
  • Strand I
  • 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


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: 1.93 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: Strand I
E: Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9076
Polymers14,7143
Non-polymers1933
Water81145
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)39.575, 39.575, 201.688
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#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.: 1 / 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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DNA chain , 2 types, 2 molecules DE

#2: DNA chain Strand I


Mass: 3686.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain Strand II


Mass: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 48 molecules

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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.8 / Details: 26 % w/v PEG 2000 MME, 0.1 M Bis-Tris 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: 0.919716 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919716 Å / Relative weight: 1
ReflectionResolution: 1.93→33.79 Å / Num. obs: 26498 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 45.14 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.029 / Net I/σ(I): 14.1
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 20.4 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1399 / CC1/2: 0.364 / % 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: 1.93→33.79 Å / SU ML: 0.2623 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2179 1308 4.95 %
Rwork0.1886 25136 -
obs0.19 26444 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.49 Å2
Refinement stepCycle: LAST / Resolution: 1.93→33.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms451 486 6 45 988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651016
X-RAY DIFFRACTIONf_angle_d0.89911453
X-RAY DIFFRACTIONf_chiral_restr0.0458156
X-RAY DIFFRACTIONf_plane_restr0.0049101
X-RAY DIFFRACTIONf_dihedral_angle_d26.3925433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.010.36321980.3532786X-RAY DIFFRACTION99.57
2.01-2.10.33371560.3132768X-RAY DIFFRACTION99.97
2.1-2.210.30751500.27752813X-RAY DIFFRACTION100
2.21-2.350.34961100.2972797X-RAY DIFFRACTION100
2.35-2.530.28551480.28462778X-RAY DIFFRACTION100
2.53-2.790.28271430.25272788X-RAY DIFFRACTION99.73
2.79-3.190.26871680.24822775X-RAY DIFFRACTION100
3.19-4.010.18831020.15132843X-RAY DIFFRACTION99.23
4.02-33.790.1451330.12462788X-RAY DIFFRACTION99.59
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)
12.3605008505356-0.287295539529860.754061671194521.0939872671911-0.344107878238420.91404785570296-0.546048937668360.75354406422770.60863431168856-0.30188950083160.507655562615460.1383983491608-0.00681369085225870.096848261748435-0.0518947488429940.12294720022908-0.091066963802717-0.0869815236630560.910981726455630.166763450937910.70354198174844-0.916882884064428.66415023670261.5946942358286
23.02666082916010.66589754639871-0.503810293000964.5181302126627-0.239409883864132.8286183569882-0.55258655155099-0.256344935463740.334408781088990.0255522863538680.31120478885610.412428255175380.012284768715251-0.833509244404470.255707420931660.345134977349670.260265773635490.0263569365845040.743680964895930.084903193303930.38581560389291-6.65844943956670.2420120577283513.493577726569
35.15614534358080.24834361348011-4.82672181452137.5377436098527-0.895675370724124.6285551588566-0.667701804858020.677509112151810.20054062902951-0.481449755435230.38710091524815-0.185695588738630.86222368474266-0.0892509815264130.241520391770310.36559181912967-0.11209832563851-0.0225836459962410.632901509488830.0286411065560420.323824075903893.3388126187617-2.7334125544455-6.14416366697
43.44137424655410.0906606233442390.109251903483061.5868982404907-0.575528885774480.58876006020854-0.67017125266021-0.276989149074390.44646560754033-0.0160239807236410.645603537662640.198576885395630.051356086466599-0.155000692220850.0302488258561480.19924799806179-0.045966508604896-0.0500155005974360.924811552484890.0733238904699290.63870810448624-1.47307416873618.09547815989452.8210872683711
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 1 through 12 )ED1 - 12
22chain 'A' and (resid 426 through 455 )AA426 - 4551 - 30
33chain 'A' and (resid 456 through 481 )AA456 - 48131 - 56
44chain 'D' and (resid 1 through 12 )DC1 - 12

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