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- PDB-8ssq: ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8ssq
TitleZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 35mer DNA 35-4
Components
  • (DNA (35-MER) Strand ...) x 2
  • 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 insulator sequence binding / regulation of centromeric sister chromatid cohesion / genomic imprinting / protein localization to chromosome, centromeric region / chromatin looping / negative regulation of gene expression via chromosomal CpG island methylation / chromosome, centromeric region / epigenetic regulation of gene expression / condensed chromosome / male germ cell nucleus ...chromatin insulator sequence binding / regulation of centromeric sister chromatid cohesion / genomic imprinting / protein localization to chromosome, centromeric region / chromatin looping / negative regulation of gene expression via chromosomal CpG island methylation / chromosome, centromeric region / epigenetic regulation of gene expression / condensed chromosome / male germ cell nucleus / transcription coregulator binding / chromosome segregation / DNA-binding transcription repressor activity, RNA polymerase II-specific / Activation of anterior HOX genes in hindbrain development during early embryogenesis / sequence-specific DNA binding / 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 / nucleolus / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
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: 3.12 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 2
D: Transcriptional repressor CTCF
E: DNA (35-MER) Strand I
F: DNA (35-MER) Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,34525
Polymers111,1876
Non-polymers1,15819
Water27015
1
A: Transcriptional repressor CTCF
B: DNA (35-MER) Strand I
C: DNA (35-MER) Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,20513
Polymers55,5933
Non-polymers61210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Transcriptional repressor CTCF
E: DNA (35-MER) Strand I
F: DNA (35-MER) Strand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,14012
Polymers55,5933
Non-polymers5469
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)352.070, 67.768, 61.194
Angle α, β, γ (deg.)90.000, 92.590, 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

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Protein , 1 types, 2 molecules AD

#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

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DNA (35-MER) Strand ... , 2 types, 4 molecules BECF

#2: DNA chain DNA (35-MER) Strand I


Mass: 10730.882 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (35-MER) Strand 2


Mass: 10806.961 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 34 molecules

#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
#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

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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: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium malonate pH 5.0, 15-22% w/v PEG 3,350 / PH range: 4.8-5.2

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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: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.12→41.86 Å / Num. obs: 49980 / % possible obs: 100 % / Redundancy: 27.1 % / CC1/2: 0.985 / Rpim(I) all: 0.076 / Net I/σ(I): 11
Reflection shellResolution: 3.12→3.23 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5013 / CC1/2: 0.397 / Rpim(I) all: 0.703 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→41.86 Å / SU ML: 0.4399 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.0806
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2714 2442 4.97 %
Rwork0.2396 46682 -
obs0.2412 49124 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 185.34 Å2
Refinement stepCycle: LAST / Resolution: 3.12→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 2856 19 15 6941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00277359
X-RAY DIFFRACTIONf_angle_d0.471710490
X-RAY DIFFRACTIONf_chiral_restr0.03131108
X-RAY DIFFRACTIONf_plane_restr0.0024858
X-RAY DIFFRACTIONf_dihedral_angle_d24.33842981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.180.41521220.38382307X-RAY DIFFRACTION82.37
3.18-3.250.36231380.36872639X-RAY DIFFRACTION92.29
3.25-3.330.34741310.35772599X-RAY DIFFRACTION94.73
3.33-3.410.34151460.33022789X-RAY DIFFRACTION97.51
3.41-3.50.3131410.29832744X-RAY DIFFRACTION98.84
3.5-3.610.32371520.29232786X-RAY DIFFRACTION99.16
3.61-3.720.28171410.28782764X-RAY DIFFRACTION99.42
3.72-3.860.36211460.25932816X-RAY DIFFRACTION99.5
3.86-4.010.31251470.25752828X-RAY DIFFRACTION99.6
4.01-4.190.28361450.24872766X-RAY DIFFRACTION99.69
4.19-4.410.29081490.23892806X-RAY DIFFRACTION99.76
4.42-4.690.23511430.232833X-RAY DIFFRACTION99.87
4.69-5.050.24831510.24422815X-RAY DIFFRACTION99.9
5.05-5.560.30421470.23322803X-RAY DIFFRACTION99.97
5.56-6.360.27921450.24662784X-RAY DIFFRACTION100
6.36-8.010.29061480.24582793X-RAY DIFFRACTION100
8.01-41.860.20531500.1772810X-RAY DIFFRACTION99.23
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)
14.67192861508-2.62281330296-1.895768087212.98960921937-1.271182392937.789049807520.468480054824-0.864998235303-0.8483974433990.8590387588030.0696264385298-1.36762716525-0.6661044719632.24388356082-0.5588117483311.49177238399-0.280128659651-0.4284682145051.722227941290.2418665235812.37337668038-24.8299740194-63.451373902668.9502966178
28.00044770129-6.040632279552.515211993995.85864260123-3.514603154092.877254301690.225710053859-0.188028924766-1.992919671730.08633959871660.3260654995270.502335493180.523559219952-0.598114112078-0.5488628887511.43978838838-0.425402026852-0.5459513302151.113801080120.3575697213311.28813821079-53.2108672659-51.862764807159.414010821
36.365918190212.40808568862-2.976030981656.084155502683.606131183145.70972082522-0.8367562404621.243815254370.151405923958-1.467315766720.839877884074-0.198937419598-1.32487531215-0.203847787918-0.07003611337252.80065199808-0.356060474194-0.7518935803572.966776498970.6395757072192.66050780459-74.8186710315-54.698476056723.81808023
48.10514071343-0.02944460516354.325235740749.00141307186.077390543038.58768021038-1.12678299776-1.808738383161.502159550763.590570932560.239344053334-2.390219429750.5707214931853.628784795790.7274437600762.40153108778-0.200027480715-0.4007664645583.734310852740.1924284714771.94266472559-22.8048097619-65.623032550775.9398919179
54.49208843201-1.336453175846.849806839082.89772146195-1.95526154349.76697405403-0.7194534633042.27633971869-1.21277590409-0.462740089681.069473907330.919054091128-0.464889252833-0.0984987912435-0.277274933881.79156763791-0.61822131665-0.3793743009582.216149886570.1549897847691.57401502322-63.5755698677-59.744247531237.4911085595
67.30808054281-4.279765284646.39625300672.58391035257-4.194161059547.0302389563-0.1241389184453.31324991783-1.98489740825-0.6926145154010.6692494499250.99930168583-0.5705360735530.893986578547-0.602565238131.99170980379-0.296249797352-0.800367117382.831911710420.01559770535672.05257509168-64.3191594329-59.206379445636.9320207624
76.86635786348-3.120326989272.048702809827.74637525751.380877399281.48152437901-0.525026491701-5.20436297173-1.502210794663.33987374250.789808598618-1.60589612759-0.5900781578522.49441561978-0.3622358562172.27868348048-0.388012316662-0.7349031240184.591981681710.6811516788432.45190519508-21.6411146657-67.248166140975.0805984358
87.03136222187-4.58706243597-1.426335828547.470146674144.679281631696.970355640091.98345697690.54261565650.148083365892-1.74438843426-0.130739560325-0.7051381029681.22975181794-1.19749423158-1.62819230232.436597688880.489626989559-0.7292784098182.27071215666-0.07637076129282.21438983046-75.7808432004-8.96929818649-8.90212205087
98.00976444148-6.88568202789-5.16874611497.349642286994.174202738776.400664494980.965449538591.67001011819-1.47442911184-0.640461095232-1.655897465463.33673595227-1.01404771894-2.672319418630.7448700518571.18174774544-0.0983424454529-0.3342907419282.54734195120.1887691729812.11520292212-76.9600018502-27.93215888625.09595267323
102.84526051851-2.22429165596-1.45222886354.694379119241.890714156667.988188165290.2719490622240.5502197446790.666157155786-0.9376589618920.6020572812280.3126793342-1.81827833851-0.394818796548-0.3048909807371.48555378245-0.472247786665-0.3174717855661.376409158210.4338045829150.546412244963-52.0540346636-23.70269353769.04711658614
112.731315424860.3618763868991.96846858751.47775523851-1.483475598177.82157290761-1.15265705510.608143848569-0.8842698420940.519065538743-0.1216272585-0.316447548202-0.124018603483-1.427197694740.4132446612280.825042770215-0.0714879542279-0.6908262007371.54048076060.4976772497530.658880263768-54.3742080141-30.110130707737.6088299089
128.70698763427-4.539679410854.14065106312.90056211839-0.8651053197115.151409877830.3698037205640.1444109561540.3783701396491.03801509177-0.201647662156-1.48717464867-0.005356446642192.05878441151-0.2585160664251.07072483526-0.0915662008037-0.5116599550211.869645865480.4521691589391.25607179082-37.9613620299-31.840992226949.9133236512
133.3914506221-3.194661685990.4536534679043.049296461290.2597981451475.351460051210.05936118061040.807122374224-1.48007283093-0.7889290789480.2691419707271.000436311910.9726721584880.00462373777402-0.476129957511.13327982244-0.0978235056481-0.7574419663031.916067467920.04686384406232.34678442929-16.7086858369-47.23350746651.6995755949
142.75476361479-4.26443508986-4.022516958557.818749289418.280394259769.27371776762.133465866490.4648506146190.681908426798-2.12242165761-1.96913383033-4.2021831485-2.10817404902-0.917826892556-0.004815757639231.75516614232-0.281797979091-0.2039875048672.240855249530.4251468708151.806712991250.699220899438-32.83099836344.9867056638
156.175887730616.01443164736-6.535944542275.86392468412-6.368685834746.917408030451.539850749942.227237163494.74947446156-0.04542852939590.7050600073160.720820388145-3.17297149889-1.42359728538-2.216378956112.721835365290.223774745452-0.2728936885972.08713190210.1122662193982.72571217723-2.54821179778-20.724479475249.6517151169
165.24573359169-4.882789957792.72699777485.88127069539-1.879129976975.52399133402-0.1668608385770.714843424731-0.375927815374-1.548586823830.03064768444171.62425441358-1.61830461497-0.6585830188980.195151803981.682152259360.0679665051234-0.7689125088331.860196821230.113258741241.45201353644-62.6211993963-26.84700037815.82628259957
176.83886381872-2.7702941615.257215015691.88757846278-3.711411759456.89510797769-1.180513180830.2481375573350.368678978289-0.414263483272-0.0944461499868-1.2453051443-1.192816558280.7058872723451.130045341941.290247116270.0710527741081-0.6191503958381.890889910180.03905289293191.61983945237-21.8933391646-33.544878226244.4801333512
187.79042048607-3.542641823370.909477784655.87210183054-2.611356558021.343638174550.7887297964241.70333573297-0.746131818741-0.0649517497816-0.391378535631-0.0286281125828-0.5900323106770.719795540072-0.3447874092821.25640082449-0.156278106202-0.8305573447572.13073638790.1103866719791.8973690104-15.169396796-34.851796316950.4918295301
197.687122060171.557500376760.6678972360195.547221649390.445148236257.71477585269-0.0131680668926-0.154080681941-0.132302496452-0.02017251614820.403881004158-0.2475545407210.2643147349610.424285939545-0.3385745110741.02252681378-0.0754746471796-0.1927768356751.060490140130.09677283315120.562974440488-44.9561457133-32.079992664621.3800179645
205.602501981842.675942245513.868640406966.471264808610.8750438656258.33385278829-0.2549251961940.0653767051278-1.08151169948-2.253898308-0.5623221370221.23275399301-1.9586883784-2.198463698590.7960475179732.259247990750.604809235592-1.013505389862.59344735913-0.06084874806562.33270978567-73.7879843957-21.5943722382-6.06484546145
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 349 through 429 )DM349 - 4291 - 81
22chain 'D' and (resid 430 through 491 )DM430 - 49182 - 143
33chain 'D' and (resid 492 through 578 )DM492 - 578144 - 230
44chain 'E' and (resid 1 through 15 )EV1 - 15
55chain 'E' and (resid 16 through 35 )EV16 - 35
66chain 'F' and (resid 1 through 20 )FW1 - 20
77chain 'F' and (resid 21 through 35 )FW21 - 35
88chain 'A' and (resid 319 through 344 )AA319 - 3441 - 26
99chain 'A' and (resid 345 through 390 )AA345 - 39027 - 72
1010chain 'A' and (resid 391 through 448 )AA391 - 44873 - 130
1111chain 'A' and (resid 449 through 478 )AA449 - 478131 - 160
1212chain 'A' and (resid 479 through 506 )AA479 - 506161 - 188
1313chain 'A' and (resid 507 through 545 )AA507 - 545189 - 227
1414chain 'A' and (resid 546 through 566 )AA546 - 566228 - 248
1515chain 'A' and (resid 567 through 578 )AA567 - 578249 - 260
1616chain 'B' and (resid 1 through 20 )BK1 - 20
1717chain 'B' and (resid 21 through 35 )BK21 - 35
1818chain 'C' and (resid 1 through 10 )CL1 - 10
1919chain 'C' and (resid 11 through 25 )CL11 - 25
2020chain 'C' and (resid 26 through 35 )CL26 - 35

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