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

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Basic information

Entry
Database: PDB / ID: 12uo
TitleBCL11B ZF2-3 in Complex with a DNA Sequence Observed in the Human Globin Locus Containing Motif TGGCCA (Oligo 4-3)-C2 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: 3.05 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
I: DNA Strand (Self-Annealing)
J: DNA Strand (Self-Annealing)
X: DNA Strand (Self-Annealing)
Y: DNA Strand (Self-Annealing)
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)38,98712
Polymers38,7258
Non-polymers2624
Water36020
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
X: DNA Strand (Self-Annealing)
Y: DNA Strand (Self-Annealing)


Theoretical massNumber of molelcules
Total (without water)7,9812
Polymers7,9812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.818, 241.077, 45.698
Angle α, β, γ (deg.)90.000, 128.239, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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
Components on special symmetry positions
IDModelComponents
11A-607-

HOH

21D-607-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 427 through 478 or (resid 479...
d_2ens_1(chain "D" and resid 427 through 480)
d_1ens_2chain "G"
d_2ens_2chain "H"
d_3ens_2chain "I"
d_4ens_2chain "J"
d_5ens_2chain "X"
d_6ens_2chain "Y"

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_1LYSLYSLYSLYSAA427 - 48010 - 63
d_2ens_1LYSLYSLYSLYSDF427 - 48010 - 63
d_1ens_2DADADGDGGG1 - 51 - 5
d_2ens_2DADADGDGHH1 - 51 - 5
d_3ens_2DADADGDGIB1 - 51 - 5
d_4ens_2DADADGDGJC1 - 51 - 5
d_5ens_2DADADGDGXD1 - 51 - 5
d_6ens_2DADADGDGYE1 - 51 - 5

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.24522405513027, -0.0078761802012897, 0.96943443747935), (-0.0092963746679598, -0.99994012631451, -0.0057724521792483), (0.9694218587403, -0.0075966816153901, -0.24528259258442)-14.138079520051, -0.21857698802899, 18.037822896497
2given(0.94457341323825, -0.015475343502144, 0.32793533012919), (-0.026464873958458, -0.9992268357821, 0.029074750200951), (0.32723184051955, -0.036142003214756, -0.9442526558892)-5.0900143406496, 39.62375274095, 32.795350231155
3given(0.22493942742436, 0.00043545818447989, 0.97437265169245), (-0.0086279479835279, -0.99995980481068, 0.002438703874016), (0.9743345485528, -0.0089553972084533, -0.22492662883092)-14.126857174031, -0.26351684411885, 17.893911053355
4given(0.53597273097181, -0.038312324590444, -0.84336551828913), (0.024182577606081, 0.99925655381104, -0.030025699092653), (0.84388887573836, -0.0043017961542929, 0.53650075485026)16.685663793897, -39.8853462465, 5.3455924454146
5given(-0.5104172409237, 0.016252481114643, -0.85977328233986), (0.015708351064487, 0.99983077380611, 0.0095745212469538), (0.85978339590543, -0.0086186198368251, -0.51058616463574)21.421694255442, -80.788554168689, 22.74522387366
6given(-0.72552401454068, 0.00094765227849947, 0.68819619751924), (-0.0090265113065831, -0.99992613500742, -0.0081392028326653), (0.6881376507781, -0.012117197872371, 0.72547897770874)-4.1598006793033, -40.083001037544, 2.1853716408104

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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.: 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
#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.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 4.12 Å3/Da / Density % sol: 70.17 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M DL-Malic acid pH 7.0, 20% w/v Polyethylene glycol 3,350

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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: 3.05→19.86 Å / Num. obs: 23548 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 47.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.065 / Net I/σ(I): 7.3
Reflection shellResolution: 3.05→3.26 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4242 / CC1/2: 0.957 / Rpim(I) all: 0.626 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX2.0_5885refinement
autoPROCdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→19.86 Å / SU ML: 0.4357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7427
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2693 650 4.57 %
Rwork0.2392 13588 -
obs0.2406 14238 60.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.24 Å2
Refinement stepCycle: LAST / Resolution: 3.05→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms874 1590 4 21 2489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382691
X-RAY DIFFRACTIONf_angle_d0.63923933
X-RAY DIFFRACTIONf_chiral_restr0.0339427
X-RAY DIFFRACTIONf_plane_restr0.0026226
X-RAY DIFFRACTIONf_dihedral_angle_d28.48481181
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.5333517332854
ens_2d_2GGX-RAY DIFFRACTIONTorsion NCS1.2603756689798
ens_2d_3GGX-RAY DIFFRACTIONTorsion NCS0.7251907249963
ens_2d_4GGX-RAY DIFFRACTIONTorsion NCS1.2968672384404
ens_2d_5GGX-RAY DIFFRACTIONTorsion NCS1.0825382605893
ens_2d_6GGX-RAY DIFFRACTIONTorsion NCS1.0691699290858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.280.371850.32661174X-RAY DIFFRACTION26.75
3.29-3.610.29961160.2821882X-RAY DIFFRACTION42.69
3.61-4.130.33071070.25122624X-RAY DIFFRACTION57.91
4.13-5.190.26681370.22843468X-RAY DIFFRACTION76.95
5.19-19.860.21332050.21874440X-RAY DIFFRACTION98.94
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)
13.07187595495713.58420760719580.397565832192684.934437277570.443904819140030.0515925266505690.38605961981201-0.65221545535460.057562843864960.56934014883168-0.22163013240197-0.79935507458657-0.75796187995994-0.098516777754557-0.330041803326341.0934510235839-0.23655223852315-0.00532683806948150.78287332269494-0.282240920630430.46393057296437-7.697075275717-9.953658921721230.545861996775
24.93598997381746.6887121830481-3.11607591074899.3776412346674-3.26496501462184.8563315146145-0.08738160765701-1.3588476973865-0.075789183811150.47428952927533-0.20489471954385-0.4610002987944-0.6771338324880.714926672835990.296212777310330.30138449088725-0.04055116631498-0.109574292712020.60894213636147-0.0384328213370610.63520614734488-8.0339557221463-13.23860117039623.591571580565
37.3124414763587-4.4421338846291-4.3350160741324.621891723131.77213971264282.9554129888151-0.290873084266330.34137360249382-0.323463744649630.18685160899973-0.0995732330172860.360958215955520.39272601381378-0.520774213000650.242115351639320.54084652460576-0.093542368188072-0.141072936841930.171511886929740.140779235564480.18367247355607-7.2957582753847-21.92608277517810.620880677576
41.0011543820590.041314402519790.571385412930682.8386164157962-1.33326095200333.39445516290310.0569753661642890.097539699056914-0.18546638909866-0.12674923357992-0.11731278917867-0.318254416046580.502276935548010.277246345112650.410260921943380.629883916925020.244561532118680.0505519877107310.127539819977310.401644110959510.24512018936922.727102515654-25.7498849399437.093303630159
50.88697389335983-0.19612211808064-0.0216821011328648.7188842015263-2.77526352194613.15910181757020.34552536938664-0.059913646995867-0.533427623492030.10707702550848-0.37033069062421-2.3755592836453-0.0900158206863860.39964611985471-0.0335703666619511.04716973101890.073557047341407-0.0837009989901230.427186451042340.188788429397651.23171996209965.3224756127783-19.27877932197319.42249584798
63.53326568094510.23636331485661.29404530484215.7700553723085-4.00677343647654.9046172978168-0.13005714777029-0.18187735372354-0.439251657995711.3078631220415-0.70678561650082-1.35625581084440.367134939768270.429359900945360.799488616367621.02682737608910.0669990570931780.018083224413970.410889276144490.143029356926141.21771548828523.5161778854361-21.30809472673520.318954194625
70.47903500193941.62045457777020.328551694723565.48983622950411.18280868954670.848372782929550.350293876139670.00011779261100496-0.418840211403430.50550272104019-0.44024971753940.49991229606120.352011700748840.0458506790152120.0748256196560662.2098273902590.411723180107730.073094404588390.625846608048470.235102549873872.21584628195632.6904245124408-61.50655968264918.277686078105
80.225421473565060.763143283233590.355056913528312.75619042685521.09238360518970.6020807990643-0.074944904103620.0584294877194640.0658117206583720.22801458206408-0.512807126489340.58931588450388-0.13594729898499-0.0526194118013190.499745315493662.16409316924010.24974658669950.160258575631690.561641692896740.209697839780142.35343851329354.2734130796798-59.29384869928519.577713987166
94.8804614630268-4.11087425578393.42476131202957.9485282869684-1.26691031747233.560309614442-0.501569656466210.19635860528264-0.16730262455880.67478014161560.20436727380509-0.329657906556040.127335269087950.0654783674518110.258729161949470.44202662140760.295035394449180.0862155149119010.973240914434340.00153439422820721.123142865268713.691098271879.65974313966173.3073786603186
103.65574830631184.4897660339292-3.57572009821498.4000219812765-6.17295451903884.5950462931123-0.094064973177607-0.61137493325807-0.60267774013040.20711334211491-0.83674505252717-0.809337333767510.077681166287071.18570634064650.996020906689310.355746593319670.055164078783042-0.0216236253957870.604073013813070.0964846631794180.649243893085576.850126553393812.9620362620444.5477291707946
117.4353282619642-6.9125439245309-5.05231626940498.75882361164417.37653868494027.80093451931180.574281233901120.24927674052902-0.45769146540057-0.42107501748571-0.32268536405886-0.03490193670116-0.39613540887366-0.56626165092318-0.169234056841470.46848811633586-0.0647921642823670.176612279833530.216446451375170.0566746146056690.50603496515417-5.50823954828821.7234511158598.4044124261586
120.56844303853976-1.71560576875390.459785893912837.6882993853295-0.526761769214121.24215257488150.35100855639104-0.290610532617140.606024065614611.343143930886-0.170269638513150.35082913989555-0.883050637790140.023903579635539-0.190283885325770.77713822386184-0.320788041570680.427249013314930.196219316813410.0752567920545390.50370076008626-6.590827234598425.40202763858718.827633880621
136.05067206716513.97617629427910.703821942932483.15527448158260.0474326635571551.48022207637790.099359228475919-0.35369100417636-0.174374644251011.6168725246277-0.35236137000355-0.032403451870412-0.692224097998510.0877561747705830.221842245163561.0375155652077-0.23813596164215-0.133653895090610.34795174237188-0.19141174945691.02145201012136.025119467300219.00818605771218.565308481073
142.56799012313970.919327480969160.649536609148361.8730715060348-0.344391220097833.22334140440330.56306942386047-0.20562953058550.311628212698050.86894309843188-0.4725384578869-1.1749334965417-0.373658562616710.405543304822680.00852934444070161.1552186789335-0.210971032161350.0206986867924370.38623281734491-0.00664744851403051.14116907229426.401167612718421.01115555946916.534786318436
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 481 )AA467 - 48041 - 54
55chain 'I' and (resid 1 through 13 )ID1 - 13
66chain 'J' and (resid 1 through 13 )JE1 - 13
77chain 'X' and (resid 1 through 13 )XF1 - 13
88chain 'Y' and (resid 1 through 13 )YG1 - 13
99chain 'D' and (resid 427 through 438 )DH427 - 4381 - 12
1010chain 'D' and (resid 439 through 450 )DH439 - 45013 - 24
1111chain 'D' and (resid 451 through 466 )DH451 - 46625 - 40
1212chain 'D' and (resid 467 through 481 )DH467 - 48141 - 55
1313chain 'G' and (resid 1 through 13 )GK1 - 13
1414chain 'H' and (resid 1 through 13 )HL1 - 13

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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