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

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Basic information

Entry
Database: PDB / ID: 12up
TitleBCL11B ZF2-3 in Complex with a DNA Sequence Observed in the Human Globin Locus Containing Motif TGGCCA (Oligo 4-2)
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
BROMIDE ION / DNA / DNA (> 10) / B-cell lymphoma/leukemia 11B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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 Top
E: Strand Bottom
F: B-cell lymphoma/leukemia 11B
G: Strand Top
H: Strand Bottom
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,24914
Polymers30,6686
Non-polymers5818
Water27015
1
A: B-cell lymphoma/leukemia 11B
D: Strand Top
E: Strand Bottom
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6247
Polymers15,3343
Non-polymers2914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: B-cell lymphoma/leukemia 11B
G: Strand Top
H: Strand Bottom
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6247
Polymers15,3343
Non-polymers2914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.167, 38.701, 59.860
Angle α, β, γ (deg.)97.109, 98.654, 99.705
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 427 through 458 or (resid 459...
d_2ens_1chain "F"
d_1ens_2chain "D"
d_2ens_2chain "G"
d_1ens_3(chain "E" and resid 2 through 13)
d_2ens_3chain "H"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1LYSLYSMETMETAA427 - 47810 - 61
d_2ens_1LYSLYSMETMETFD427 - 47810 - 61
d_1ens_2DGDGDCDCDB1 - 71 - 7
d_2ens_2DGDGDCDCGE1 - 71 - 7
d_1ens_3DGDGDGDGEC22
d_2ens_3DGDGDGDGHF22

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.99529062282035, 0.022237929649087, 0.094350678910126), (0.021729160705511, -0.99974330376912, 0.0064163964838949), (0.094469146820079, -0.0043360181880059, -0.99551834701595)3.2261184385342, 7.5826285070898, -80.361315333786
2given(0.99492638164841, 0.024535080373095, 0.097568052820029), (0.025579002394808, -0.99962801548847, -0.0094628371577517), (0.097299587545337, 0.01191051979023, -0.99518386732394)3.6125697918004, 6.6751037480969, -80.588667635222
3given(0.99362168006698, 0.040828705168406, 0.1051140986507), (0.042128879945077, -0.99906034364935, -0.010177780790537), (0.1045997819092, 0.014541202891037, -0.99440808476351)3.8162076270592, 6.5717574027675, -80.630328165647

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Components

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Protein , 1 types, 2 molecules AF

#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.: 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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DNA chain , 2 types, 4 molecules DGEH

#2: DNA chain Strand Top


Mass: 3951.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain Strand Bottom


Mass: 3991.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 23 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn
#5: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 30% w/v Polyethylene glycol monomethyl ether 2,000, 0.15 M Potassium bromide

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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: 2.83→34.15 Å / Num. obs: 14314 / % possible obs: 99.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 7.7 Å2 / CC1/2: 0.996 / Net I/σ(I): 3.4
Reflection shellResolution: 2.83→2.88 Å / Num. unique obs: 658 / CC1/2: 0.453

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Processing

Software
NameVersionClassification
PHENIX2.0_5885refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→34.15 Å / SU ML: 0.3998 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.9539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2872 460 4.64 %
Rwork0.2344 9445 -
obs0.2369 9905 68.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.59 Å2
Refinement stepCycle: LAST / Resolution: 2.83→34.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 1036 8 16 1878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00362011
X-RAY DIFFRACTIONf_angle_d0.58982903
X-RAY DIFFRACTIONf_chiral_restr0.0332317
X-RAY DIFFRACTIONf_plane_restr0.003193
X-RAY DIFFRACTIONf_dihedral_angle_d28.5454843
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.87137980385899
ens_2d_2BDX-RAY DIFFRACTIONTorsion NCS0.29503592728954
ens_3d_2CEX-RAY DIFFRACTIONTorsion NCS0.49607859186149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-3.240.3937450.29791091X-RAY DIFFRACTION23.66
3.24-4.080.33532120.2413790X-RAY DIFFRACTION83.24
4.08-34.150.22012030.2164564X-RAY DIFFRACTION98.49
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)
11.0703811428583-0.288906953342880.00592480633973890.435391669206230.212889517310650.13546889123434-0.12868485624129-0.233970921931240.191835796090080.0776830439839270.0865810273780730.042242447789875-0.00060087978343005-0.036248235818250.0216055944700640.451391463929880.296035932560520.0987869761728160.927767700593060.252887967916920.94107066195781-9.953980383166814.497539397283-64.589419723884
28.2089980717519-2.36561227544632.34188704761426.06625109213711.52696150948612.6673956335502-0.014381552315611-0.41354653421917-0.202541957623660.0280824470316120.0216081600436010.509066971490450.10330303984943-0.39965450649935-0.0584964527563240.2528547439012-0.052663095112933-0.0976968180439440.596227194081410.29086129548460.59113000430811-3.088198855198710.203710759546-64.481991692388
32.41522615743080.23506649402198-0.128107727125492.0824712652249-0.583431909954472.5718607937363-0.02146791741428-0.00219738723722760.026044092230316-0.0260048844170970.00648643714676820.151120631520510.068294856616708-0.082329571687527-0.0436379710651370.21727529959116-0.143749200725030.0821203312426040.3962402165870.0423760684812210.452256331772595.51909189289294.6950249323995-64.407221073898
42.77601868912020.69119156416921.50888267558820.430449642798580.761869495240231.39729937922070.0620119419151950.073495259585693-0.46780605147630.0967245295964890.082546930235216-0.187299487993920.185818143153970.26181285036643-0.111563879583570.2155160980941-0.01151541298291-0.0827862791577130.428162830450420.218021598345110.6570017769210413.4065598482693.1001253152151-60.5604798655
50.610699598961320.176935861193290.223413745267722.3329965855638-1.39411172845876.9840965122004-0.126260871641490.229875702143160.19276905286330.11117012638619-0.29196323124894-1.2968300753386-0.0813963507427740.843532106414530.495284623457630.45624711841458-0.0232294443976060.147751351532510.265329103108170.0831621641191030.7508330924126315.4010340925269.449296765734-55.421322254893
60.1787564338372-0.027101448390565-0.241433645429290.00376466690381750.0358162681321840.325298292890410.045851909455376-0.095723300798788-0.0655536515362040.40905384793509-0.0139279688236790.24865472077955-0.16228059188947-0.070232022166971-0.396798740048120.72060804774314-0.0573652125532570.0658640906496590.4979861484590.335035062042360.563157354946614.612897483056113.454927279421-53.102251838694
71.05337961869940.4282474776346-1.39645007984411.0041881952986-0.416091330837441.87854232918970.21410945587524-0.0753295274475470.127955349653870.1276370442150.0153701034005120.08549011538476-0.28810434982753-0.0118169159571620.122397354910190.79118169694010.0199698144315990.0205852235953220.481961547081840.276941954259540.442428863166065.440154659689716.396615736001-54.275597214666
82.26635303545550.32714411506906-0.441327403555851.6030931833608-0.279824066489261.3926956484265-0.173650541880850.280065626199880.03109779412208-0.009701141135565-0.042947256730010.340173781299970.1217009224808-0.297774330505050.106993872278220.26425100060088-0.14228275891567-0.069328601338770.430881081199570.146647465350050.68519620696546-6.8129509234579-3.668678812329-16.684753417766
91.53448793293590.19216713791725-0.469744351796850.650375128820650.316871636504650.36895458223538-0.334342018636420.496252857501720.83619481401618-0.037392312040489-0.005242806024461-0.45440019095671-0.404497778088330.949394236367830.306908181635790.55635993095338-0.1480355795264-0.309792181225681.12763812624960.415461722838940.9965669373072312.0456653624150.91775967851909-21.36729007281
100.64012407837532-0.37527200267449-0.22001066541940.38198162524564-0.238071387593430.90974122166088-0.146312406687170.0364862433404360.12965697473263-0.454172954424270.0665733394168590.09838657109626-0.138304584431250.147445791459150.0508768418322340.973183004569490.0422757604642560.0411879333135820.711622184737650.429869629159720.657006652902663.3521023169162-6.1488432728321-27.134310982309
111.0723123152947-0.828684726980011.54702252140932.3020201440397-0.732509541090412.41045706100920.072090011417316-0.16589691515659-0.24616262629623-0.19300629549482-0.086965428435734-0.152850238145410.650366423874470.279555412281530.0357301890657570.95640059254392-0.0571436071805010.124540747647470.739382680839550.367194250627110.583751139055643.7412437162194-9.803054008867-24.864887183677
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 426 through 438 )AA426 - 4381 - 13
22chain 'A' and (resid 439 through 450 )AA439 - 45014 - 25
33chain 'A' and (resid 451 through 455 )AA451 - 45526 - 30
44chain 'A' and (resid 456 through 466 )AA456 - 46631 - 41
55chain 'A' and (resid 467 through 478 )AA467 - 47842 - 53
66chain 'D' and (resid 1 through 13 )DB1 - 13
77chain 'E' and (resid 1 through 13 )EC1 - 13
88chain 'F' and (resid 427 through 455 )FD427 - 4551 - 29
99chain 'F' and (resid 456 through 478 )FD456 - 47830 - 52
1010chain 'G' and (resid 1 through 13 )GE1 - 13
1111chain 'H' and (resid 2 through 13 )HF2 - 13

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