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- PDB-8ssr: ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA... -

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Basic information

Entry
Database: PDB / ID: 8ssr
TitleZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-20
Components
  • DNA (35-MER) Strand I
  • DNA (35-MER) Strand II
  • Transcriptional repressor CTCF
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN / transcription factor / zinc fingers / insulator/chromatin architecture / transcription-dna complex / TRANSCRIPTION
Function / homology
Function and homology information


chromatin loop anchoring activity / chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / protein localization to chromosome, centromeric region / genomic imprinting / chromatin looping / cardiac muscle cell development / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / chromosome, centromeric region ...chromatin loop anchoring activity / chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / protein localization to chromosome, centromeric region / genomic imprinting / chromatin looping / cardiac muscle cell development / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / chromosome, centromeric region / condensed chromosome / epigenetic regulation of gene expression / transcription coregulator binding / male germ cell nucleus / mitochondrion organization / chromosome segregation / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific double-stranded DNA binding / gene expression / sequence-specific DNA binding / in utero embryonic development / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / 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) / Transcriptional repressor CTCF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsHorton, J.R. / Yang, J. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structures of CTCF-DNA complexes including all 11 zinc fingers.
Authors: Yang, J. / Horton, J.R. / Liu, B. / Corces, V.G. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional repressor CTCF
B: DNA (35-MER) Strand I
C: DNA (35-MER) Strand II
D: Transcriptional repressor CTCF
E: DNA (35-MER) Strand I
F: DNA (35-MER) Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,34325
Polymers111,1856
Non-polymers1,15819
Water00
1
A: Transcriptional repressor CTCF
B: DNA (35-MER) Strand I
C: DNA (35-MER) Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,22714
Polymers55,5923
Non-polymers63511
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Transcriptional repressor CTCF
E: DNA (35-MER) Strand I
F: DNA (35-MER) Strand II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,11611
Polymers55,5923
Non-polymers5238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)362.211, 68.090, 61.988
Angle α, β, γ (deg.)90.000, 94.870, 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

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Components

#1: Protein Transcriptional repressor CTCF / 11-zinc finger protein / CCCTC-binding factor / CTCFL paralog


Mass: 34055.461 Da / Num. of mol.: 2 / Fragment: Zinc finger domains 3-11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P49711
#2: DNA chain DNA (35-MER) Strand I


Mass: 10754.907 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (35-MER) Strand II


Mass: 10781.948 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
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: 3.43 Å3/Da / Density % sol: 64.09 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 20-25%% w/v PEG 3,350, 0.1 M BIS-TRIS pH 5.0-6.5, 0.05-0.20M NaCl
PH range: 5.0-6.5

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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: Nov 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.14→37.59 Å / Num. obs: 46861 / % possible obs: 95.7 % / Redundancy: 15.8 % / Biso Wilson estimate: 107.65 Å2 / CC1/2: 0.94 / Rpim(I) all: 0.061 / Net I/σ(I): 10.9
Reflection shellResolution: 3.14→3.26 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3269 / CC1/2: 0.883 / Rpim(I) all: 0.338 / % possible all: 73.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→37.59 Å / SU ML: 0.4676 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.3208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2841 2353 5.05 %
Rwork0.2492 44203 -
obs0.2509 46556 90.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 203.25 Å2
Refinement stepCycle: LAST / Resolution: 3.14→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 2856 19 0 6926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00277359
X-RAY DIFFRACTIONf_angle_d0.480710490
X-RAY DIFFRACTIONf_chiral_restr0.03141108
X-RAY DIFFRACTIONf_plane_restr0.0023858
X-RAY DIFFRACTIONf_dihedral_angle_d24.59682981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.210.3618590.37241087X-RAY DIFFRACTION37.52
3.21-3.280.37561060.37461880X-RAY DIFFRACTION64.67
3.28-3.350.35491110.37672075X-RAY DIFFRACTION74.23
3.35-3.440.40031300.37622469X-RAY DIFFRACTION84.03
3.44-3.530.37721350.36122545X-RAY DIFFRACTION90.6
3.53-3.630.34931450.342725X-RAY DIFFRACTION94.56
3.63-3.750.34811450.31542747X-RAY DIFFRACTION96.18
3.75-3.880.29721530.29962863X-RAY DIFFRACTION99.11
3.88-4.040.30881520.27412881X-RAY DIFFRACTION99.93
4.04-4.220.33581510.27242833X-RAY DIFFRACTION99.97
4.22-4.440.34911520.26312898X-RAY DIFFRACTION99.97
4.45-4.720.25991550.25432866X-RAY DIFFRACTION99.97
4.72-5.090.25671540.2452848X-RAY DIFFRACTION99.97
5.09-5.60.28331540.24562891X-RAY DIFFRACTION100
5.6-6.40.3231500.26092850X-RAY DIFFRACTION100
6.4-8.050.26711520.24592861X-RAY DIFFRACTION100
8.06-37.590.21831490.16832884X-RAY DIFFRACTION99.61
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)
13.34305648087-2.251541761362.032869208512.846215736180.8517318681825.171747779221.580380322421.855320293830.0615185767443-5.1214169460.8155430032120.747919139815-0.915253102361.20720641089-1.968312839415.369712648560.203049125853-0.8517964373052.38959297686-0.06294110269392.04033911547-76.9158245457-8.41222342576-8.93858308945
21.03410074427-1.23029592608-2.773544380045.31931710612.816351528676.14061020243-0.09952656948960.263641736357-0.146164544138-0.185375117983-0.7072724505472.19778086378-1.24549803829-1.934949283160.4179040852470.933580382421-0.396905816371-0.4635835354842.341510328460.2198882332681.93078690447-79.1242719854-27.30405842175.04712656467
33.39590229264-1.96185637882-2.479195144255.7329730914-0.08303309569932.460459415540.409829508980.835941996070.0966229926029-2.194698312530.4234253414532.19481840739-1.242243409-0.245292763552-0.958769610941.67914290257-0.499572671021-0.1705910260321.352352631460.2416775252050.473185965927-54.8163843-26.66238594142.57394880622
41.28065727466-0.0703472095268-1.058660458055.10368583625-0.163065291696.54151392347-0.2262341777520.0994641500989-0.127959078554-0.04368390098440.230354002128-0.950157593947-2.24348751048-0.280468802225-0.006594625667171.11617838065-0.102565286071-0.2042109371741.261019114840.4368371470770.690780647224-55.5596931041-24.232042203232.2895697579
55.58718048457-3.505956602485.071961417092.18840297468-3.175383277144.70909439527-0.6377869517930.3404783794580.1907602159790.3986555360750.762251507663-1.65921911367-0.1356545689781.177522329790.2187842946410.8809779256290.098388455191-0.5642319902931.710756823480.2167994771711.45963649535-41.0831167993-31.290279239150.112295323
67.18816001024-5.55332949277-1.026483553694.35044271507-0.03987085917774.91077551470.62870754871.31502744425-1.45143976305-0.849040858038-0.3291453746540.274502333480.0971910556593-0.476019777405-0.2062793872361.01279850051-0.107755613954-0.4813272329061.30790065068-0.06635381503771.52641771405-13.3113620945-41.95145447950.1332793764
72.028545504361.96624774261-0.7654794823739.869062386592.478531949563.181199311753.861300133121.559006886971.476752508081.938035587770.309272706071-1.091269239460.272030744733-0.722515040539-4.321631723452.463725532930.133746252320.03703456578342.259883048710.440376349892.71497996948-4.18676056336-20.228320373150.2151428566
84.84567370945-3.113120130814.338557149492.86809565135-3.938527106095.14526823660.505349243232-0.348761762049-1.68689312583-1.608456329640.2522696292192.71168636387-1.73933303941-2.25556430131-0.4237312194353.067022273830.270934296689-1.587941698462.328354439780.1822629912172.23088005037-71.3215454288-23.83025906581.29365328901
99.128866374610.5247336446656.663392635850.651686261546-1.757915232024.72549739117-0.7671657923630.00399561086834-0.5921123518680.260271121330.463425157027-1.26356527646-0.7876527094860.6816535834070.5018979524471.275867751950.0703364143519-0.5316816942942.01323090665-0.03898728646361.5863502102-29.7441000955-33.024556605238.520951741
104.21212729267-3.271572845952.850647625538.267940206731.137312521564.95484680920.9312830883621.51562295613-0.872728615712-0.567567902565-0.4088852309350.4717030837020.1630349152071.00456310332-0.1652854568511.15497746241-0.278635771296-0.7778672741622.423656510090.343884752482.16148942657-17.7200460985-34.221544952651.0909727831
115.00005446156-0.5208484834691.989523969726.36140122456-0.2166506631225.13924779283-0.714175770584-0.136557392419-0.4583948307690.3650874548420.938743317216-0.557276746184-0.6634760274380.982413654298-0.04270945014011.21199472526-0.0698735305831-0.1210210178241.370799846060.02724818831480.570919051689-47.1432394737-31.551658079921.6377501642
122.814347608540.9255506101390.5021340604415.98291851854-2.924399120022.97933312942-1.02613089693-0.470438668738-0.773061089806-2.24818913378-0.7175676859330.032023185488-3.02303145376-1.565416862361.570110723193.311767616070.668325566258-1.251597358982.53910474813-0.1391867875412.2306854292-75.9017907269-21.3348106657-5.98721432918
130.759643589215-0.397158994354-0.03550649471540.258740859651-0.08370393555470.0955758648327-1.3636400291-0.5500155905010.7600118459864.992764298390.612992801604-0.711446829675-1.917343185430.847708030920.7040341415516.2469535121-1.02263215467-0.9379579389452.377833045880.407124341473.5973511565-20.3832635405-51.458721861780.0588484859
143.381259111122.57626512022-0.9057557113473.74761495923-4.416274317958.082186715371.40100019504-4.05430188599-0.6641357161721.90152418357-2.07989088862-0.568441066019-2.019620058112.663966517880.6583855745691.36899711456-0.662426146697-0.1623945548043.46909428581-0.1972809835091.99121948089-21.79530738-61.557739977463.3623567381
153.853212843926.021478102270.4342421654689.415128139270.6754648123286.01220363598-1.08091891331.24426446675-0.5351920427610.4456863266821.11541553458-0.3031443962050.4598871869921.161348499940.6428152982861.67222519732-0.570222261407-1.289641964730.1128077074150.9067493162843.93866646445-38.3915190859-76.276860673466.098030075
165.94242836598-2.716430818561.615062451255.90765028143-4.895870954153.88661351217-0.7640104518790.0583487983421-2.96778677972-1.263525209230.132878109175-1.128883621251.09749316426-0.00160436600333-0.33106323621.48398104502-0.38594374176-1.057968488190.9151396461720.5223888866211.02321192806-54.8170132342-52.55353595461.4771651657
171.483198012282.2556065914-2.363998568837.82455586023-6.144285165415.701161091461.405302284640.68787548451-0.983076597716-2.389176951550.6085229913054.127517684451.67832715442-1.27201732705-1.098560693031.67013427543-0.401578114643-0.9290287693111.066328914130.2677657132881.71737526426-64.5811247837-47.735598330653.7325103209
184.2989470446-3.04571117727-1.218075813312.874650731150.8004278902965.339764538010.1927623999971.375439328781.32059471562-0.3104024086120.270340349736-1.17397441303-0.317122803997-0.374486230669-0.3659190718891.98171083345-0.590980176147-0.8153264500471.974567784360.5982701680422.49341831133-72.44968014-46.822753327425.8734321981
195.7365240841-3.345720323483.734051788883.708667976820.6622056058737.27712504542-1.083949074380.553258068378-1.687387794250.2387324621431.449305946-0.431534963074-0.6071899712742.72657242882-0.8301160083062.05554676129-0.469479734634-0.8640862437372.15826038771-0.04089530855412.23402650571-86.8257395244-68.685426773621.2289756438
205.28673050954-1.598227127881.699612641498.060166355221.645003412341.126104541-0.979843592099-0.983958357183-0.264077346363-0.2816045391052.03603630315-0.750557292413-2.10307008248-1.51934329436-1.283682175313.495941675460.2748495275560.03445839278152.82470295630.6106156147092.28772518167-19.8992345484-67.209680144181.8752560777
217.625488733250.5344347952175.171417313862.94504927928-0.5211937264127.211805635-0.7188130118440.7857515937630.683913976546-0.4993738428860.1899924724230.401367910276-0.0825304676696-0.8324241918810.3169001427851.72190230007-0.391685798114-0.2889701794821.50149042782-0.1107496485181.46549055982-61.353904273-59.565971731143.5492027867
227.37785689703-0.2139214421236.139639800274.157020035530.6357286044367.69629959316-0.95536038892.911512896090.774314234297-0.112399266141-0.746857167131-1.08494080951.500027926360.1061869026851.664024926332.47661224742-0.858495205369-0.6954203088972.755603962790.1434861989391.81461044871-79.8335123777-55.47410172927.1338349211
233.62239105114-0.634805623857-3.791704831536.32195003868-2.979959408817.23221304174-0.597852576625-0.36704822625-1.231371740050.1737218496340.360531887649-0.157784778782-1.790367079620.5539775997220.1152269345671.51390118153-0.152861577191-0.7318906360941.118109428330.139306585731.88185615311-42.967517086-62.887016661959.7787680976
245.733530455951.80753172904-7.264016948990.566681400186-2.298563604329.21330595492-2.30673233418-2.34632597203-2.12125588194-0.224615983106-2.42914105086-2.14943433222-3.8103892343-1.627974498694.730603851393.23471295289-0.153926212228-0.8269573083436.142331633820.7425217028423.11444406005-11.7699066245-72.11409223584.2971157894
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 319 through 344 )AA319 - 3441 - 26
22chain 'A' and (resid 345 through 390 )AA345 - 39027 - 72
33chain 'A' and (resid 391 through 429 )AA391 - 42973 - 111
44chain 'A' and (resid 430 through 478 )AA430 - 478112 - 160
55chain 'A' and (resid 479 through 506 )AA479 - 506161 - 188
66chain 'A' and (resid 507 through 566 )AA507 - 566189 - 248
77chain 'A' and (resid 567 through 578 )AA567 - 578249 - 260
88chain 'B' and (resid 1 through 15 )BK1 - 15
99chain 'B' and (resid 16 through 35 )BK16 - 35
1010chain 'C' and (resid 1 through 10 )CL1 - 10
1111chain 'C' and (resid 11 through 25 )CL11 - 25
1212chain 'C' and (resid 26 through 35 )CL26 - 35
1313chain 'D' and (resid 349 through 373 )DM349 - 3731 - 25
1414chain 'D' and (resid 374 through 402 )DM374 - 40226 - 54
1515chain 'D' and (resid 403 through 429 )DM403 - 42955 - 81
1616chain 'D' and (resid 430 through 478 )DM430 - 47882 - 130
1717chain 'D' and (resid 479 through 491 )DM479 - 491131 - 143
1818chain 'D' and (resid 492 through 545 )DM492 - 545144 - 197
1919chain 'D' and (resid 546 through 578 )DM546 - 578198 - 230
2020chain 'E' and (resid 1 through 10 )EV1 - 10
2121chain 'E' and (resid 11 through 35 )EV11 - 35
2222chain 'F' and (resid 1 through 10 )FW1 - 10
2323chain 'F' and (resid 11 through 30 )FW11 - 30
2424chain 'F' and (resid 31 through 35 )FW31 - 35

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