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

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Basic information

Entry
Database: PDB / ID: 12ul
TitleBCL11B ZF2-3 in Complex with a DNA Sequence Observed in the Human Globin Locus Containing Motif TGTCCA (Oligo 3-4)
Components
  • B-cell lymphoma/leukemia 11B
  • Strand Bottom
  • Strand Top
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: 2.81 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
E: Strand Top
F: Strand Bottom
A: B-cell lymphoma/leukemia 11B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6508
Polymers15,3333
Non-polymers3175
Water41423
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)50.486, 50.486, 169.298
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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DNA chain , 2 types, 2 molecules EF

#1: DNA chain Strand Top


Mass: 3926.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain Strand Bottom


Mass: 4015.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 1 types, 1 molecules A

#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.: 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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Non-polymers , 3 types, 28 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-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.: 23 / 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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 28% PEG 4000, 0.1M TRIS-HCl pH 8.0

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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: 0.919716 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919716 Å / Relative weight: 1
ReflectionResolution: 2.81→33.89 Å / Num. obs: 11712 / % possible obs: 100 % / Redundancy: 25.2 % / Biso Wilson estimate: 36.44 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.075 / Net I/σ(I): 10.5
Reflection shellResolution: 2.81→2.86 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 896 / CC1/2: 0.637 / Rpim(I) all: 1.68

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Processing

Software
NameVersionClassification
PHENIX2.0_5885refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→32.89 Å / SU ML: 0.2326 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2601 381 4.59 %
Rwork0.2255 7918 -
obs0.2272 8299 81.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.94 Å2
Refinement stepCycle: LAST / Resolution: 2.81→32.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms437 527 14 23 1001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341054
X-RAY DIFFRACTIONf_angle_d0.5351509
X-RAY DIFFRACTIONf_chiral_restr0.029162
X-RAY DIFFRACTIONf_plane_restr0.002100
X-RAY DIFFRACTIONf_dihedral_angle_d26.1636452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-3.220.3204760.3381480X-RAY DIFFRACTION46.01
3.22-4.050.31521530.24463206X-RAY DIFFRACTION99.03
4.05-32.890.20511520.18333232X-RAY DIFFRACTION99.71
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)
10.303452692770580.2376305642684-0.445410314106430.906195427770180.447293216531471.52518571595260.182336621546740.14193671769209-0.19519375452555-0.195883983328920.19281677209331-0.014208030718936-0.261294490203150.18296578451289-0.210350337250370.651093919938660.037687995761628-0.246479703587540.824508575128040.0588942031761910.1882686074271-0.943854892072424.942737051909-21.379437000493
20.563497687785990.25448788891756-1.24316428804552.94506381262940.818415407070583.5425508157730.011318956003177-0.232828558361910.121432595888180.172655297241920.15096368267170.31325656370666-0.50410076736344-0.80763676730373-0.114926403534990.502373306889680.0237171098575470.0320055104930940.76786632095259-0.017453683845930.10319888147292-2.008096129425825.038294685962-17.792995054262
34.00560535474820.21210424270847-0.0630869059364450.12451492229579-0.198165701124950.53704425753024-0.016294481392314-0.954057653416350.744194170520410.220773126865360.097626772782201-0.26606861387304-0.197270157673440.35034161460793-0.0284494268118740.0901748010127120.070977168162574-0.0474125132276780.59759147161722-0.21498865515780.4152953648233810.18990684242323.834976722284-11.933616299995
43.52222748634460.57884880598344-0.26318769817131.64259813394460.230545187000721.3277403624141-0.0428954085912910.34361797529124-0.11006771751961-0.0515462912634760.0102779742650840.210157132980850.042667585214299-0.0985617940994970.0587267739416950.0077428151110660.0541154145366740.114017654742180.47304057036241-0.00382981929431850.34596899825823-3.245150243726912.392634471664-24.912327630222
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 13 )EA1 - 13
22chain 'F' and (resid 1 through 13 )FB1 - 13
33chain 'A' and (resid 427 through 455 )AE427 - 4551 - 29
44chain 'A' and (resid 456 through 480 )AE456 - 48030 - 54

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