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- PDB-7txc: HIC2 zinc finger domain in complex with the DNA binding motif-2 o... -

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Basic information

Entry
Database: PDB / ID: 7txc
TitleHIC2 zinc finger domain in complex with the DNA binding motif-2 of the BCL11A enhancer
Components
  • DNA (5'-D(*AP*CP*TP*GP*TP*TP*GP*GP*CP*AP*TP*TP*AP*TP*CP*T)-3')
  • DNA (5'-D(*AP*GP*AP*TP*AP*AP*TP*GP*CP*CP*AP*AP*CP*AP*GP*T)-3')
  • Hypermethylated in cancer 2 protein
KeywordsDNA BINDING PROTEIN/DNA / zinc-finger domain / gene expression / DNA BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


: / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Hypermethylated in cancer 2 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.04 Å
AuthorsHorton, J.R. / Ren, R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: Nat.Genet. / Year: 2022
Title: HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription.
Authors: Huang, P. / Peslak, S.A. / Ren, R. / Khandros, E. / Qin, K. / Keller, C.A. / Giardine, B. / Bell, H.W. / Lan, X. / Sharma, M. / Horton, J.R. / Abdulmalik, O. / Chou, S.T. / Shi, J. / ...Authors: Huang, P. / Peslak, S.A. / Ren, R. / Khandros, E. / Qin, K. / Keller, C.A. / Giardine, B. / Bell, H.W. / Lan, X. / Sharma, M. / Horton, J.R. / Abdulmalik, O. / Chou, S.T. / Shi, J. / Crossley, M. / Hardison, R.C. / Cheng, X. / Blobel, G.A.
History
DepositionFeb 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*AP*TP*AP*AP*TP*GP*CP*CP*AP*AP*CP*AP*GP*T)-3')
B: DNA (5'-D(*AP*CP*TP*GP*TP*TP*GP*GP*CP*AP*TP*TP*AP*TP*CP*T)-3')
E: Hypermethylated in cancer 2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8046
Polymers23,6083
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-27 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.237, 114.237, 59.146
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: DNA chain DNA (5'-D(*AP*GP*AP*TP*AP*AP*TP*GP*CP*CP*AP*AP*CP*AP*GP*T)-3')


Mass: 4915.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*AP*CP*TP*GP*TP*TP*GP*GP*CP*AP*TP*TP*AP*TP*CP*T)-3')


Mass: 4879.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Hypermethylated in cancer 2 protein / Hic-2 / HIC1-related gene on chromosome 22 protein / Hic-3 / Zinc finger and BTB domain-containing protein 30


Mass: 13813.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIC2, HRG22, KIAA1020, ZBTB30 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon-Plus / Variant (production host): RIL / References: UniProt: Q96JB3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 4.72 Å3/Da / Density % sol: 73.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 18% Tacsimate pH7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.04→37.94 Å / Num. obs: 16302 / % possible obs: 98.6 % / Redundancy: 10.1 % / Biso Wilson estimate: 63.91 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.048 / Net I/σ(I): 13.5
Reflection shellResolution: 3.04→3.16 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1640 / CC1/2: 0.895 / CC star: 0.972 / Rpim(I) all: 0.299 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.04→37.94 Å / SU ML: 0.1922 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1267
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2093 814 5.01 %
Rwork0.1925 15437 -
obs0.1934 16251 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.52 Å2
Refinement stepCycle: LAST / Resolution: 3.04→37.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms650 650 3 0 1303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361397
X-RAY DIFFRACTIONf_angle_d0.60442022
X-RAY DIFFRACTIONf_chiral_restr0.0334220
X-RAY DIFFRACTIONf_plane_restr0.0047148
X-RAY DIFFRACTIONf_dihedral_angle_d26.2967553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.230.29881310.25222543X-RAY DIFFRACTION96.67
3.23-3.480.25671340.22182647X-RAY DIFFRACTION99.64
3.48-3.830.281290.25992380X-RAY DIFFRACTION91.94
3.83-4.390.23251380.22462637X-RAY DIFFRACTION99.82
4.39-5.520.19311380.19162598X-RAY DIFFRACTION100
5.53-37.940.16021440.13462632X-RAY DIFFRACTION99.75
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)
11.247728868380.0754000475220.1529160669240.580459974033-0.3429166833430.2396413600520.009085134459250.4770240797460.117799980689-0.3977268959460.1238239458230.000184113438582-0.009898528598760.1140554022730.2160875143762.234856792590.1227015076880.2345511907961.405887074180.9051213087540.32388755830761.9190748795-6.03959325444-4.35643238476
24.896536848740.822748968524-0.856728278218.23851682344-6.223703931378.489933605140.226396736921-0.1637395971740.142076604551-0.717492474933-0.06871817264080.685229202250.981747551408-0.650006728937-0.1037823908251.03002540547-0.1377590097090.1308809044770.7000735861110.04456762324530.40472467332651.3327659963-18.837135917517.3086840187
34.608998278443.87806286348-3.137818393776.5298942970.4121891426196.082089893570.7629241202190.9247303856560.9550576604660.324169757908-0.341728521270.236975409128-0.106691002913-1.326391009-0.3955622287840.9274867642320.05277106166280.02682618984580.7388998105050.1813638644430.43851564984743.9005422005-21.378150126424.3952410282
41.97526234130.3380240252230.1191935437954.56207923431-1.497440910930.535818145739-0.1716080927961.800893215050.880198699273-1.054625818620.1904414296390.760810093514-0.655524581078-0.406307889695-0.1121269228331.77630261671-0.06376261707610.05711117126551.030171223060.289912733530.2018962041856.1035471471-11.57469925154.85381250492
58.048329065691.34234380118-4.829923501621.85468860214-2.494841869394.65833979174-0.697300764378-1.18439715403-1.109644723750.6481859365860.31295689304-0.01722901248853.181187314150.4045560338820.5390188650952.47611897340.252950070730.3598434038630.913332384998-0.03528356410040.56243375776564.9240837421-30.988582046119.657971362
64.1683244161-3.3659026291-3.734002383157.691209000563.567308458644.962497034420.165808632088-0.4011843356050.9635347340580.8110807277920.496917685628-0.158609481533-0.1928391066070.308382790694-0.6867388914561.25928909148-0.07348342638330.1250288229840.470486184103-0.03950900455860.39598329613761.5219744286-8.5693585605616.681264728
77.04663307889-3.946042416755.630741321768.42686540182.339629702219.367865804470.575748066004-0.5558422921911.22967865037-0.0363723767229-0.3465133211622.37191433210.622541554416-1.57822109421-0.281794277280.82020633649-0.09080069677470.06250407031380.8549089937470.2336332980281.2113757591739.3405512897-10.279761695416.7846046949
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 5 )AA1 - 5
22chain 'A' and (resid 6 through 16 )AA6 - 16
33chain 'B' and (resid 21 through 25 )BB21 - 25
44chain 'B' and (resid 26 through 36 )BB26 - 36
55chain 'E' and (resid 505 through 528 )EC505 - 5284 - 27
66chain 'E' and (resid 529 through 560 )EC529 - 56028 - 59
77chain 'E' and (resid 561 through 585 )EC561 - 58560 - 84

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