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- PDB-5kkq: Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex s... -

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Basic information

Entry
Database: PDB / ID: 5kkq
TitleHomo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex structure
Components
  • DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*A)-3')
  • DNA (5'-D(*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3')
  • Transcriptional repressor CTCF
KeywordsTRANSCRIPTION/DNA / CTCF / zinc finger / TRANSCRIPTION-DNA complex
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
C2H2-type zinc-finger domain / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.744 Å
AuthorsHashimoto, H. / Wang, D. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245 United States
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA.
Authors: Hashimoto, H. / Wang, D. / Horton, J.R. / Zhang, X. / Corces, V.G. / Cheng, X.
History
DepositionJun 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 (5'-D(*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*A)-3')
D: Transcriptional repressor CTCF
E: DNA (5'-D(*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,57416
Polymers55,9206
Non-polymers65410
Water5,891327
1
A: Transcriptional repressor CTCF
B: DNA (5'-D(*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3')
C: DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2878
Polymers27,9603
Non-polymers3275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-43 kcal/mol
Surface area12760 Å2
MethodPISA
2
D: Transcriptional repressor CTCF
E: DNA (5'-D(*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2878
Polymers27,9603
Non-polymers3275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-43 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.994, 44.911, 86.797
Angle α, β, γ (deg.)98.33, 92.40, 94.80
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 17541.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Plasmid: pXC1551 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL-codon plus / References: UniProt: P49711
#2: DNA chain DNA (5'-D(*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3')


Mass: 5140.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*A)-3')


Mass: 5278.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) PEG 3350, 0.2 M NaCl, 0.1 M Bis-tris, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.27046 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 5, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27046 Å / Relative weight: 1
ReflectionResolution: 1.74→28.94 Å / Num. obs: 110968 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.4
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 1.6 / % possible all: 64.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2257: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.744→28.936 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 3864 3.49 %Random
Rwork0.1704 ---
obs0.1714 110863 89.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.744→28.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 1382 10 328 4104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174139
X-RAY DIFFRACTIONf_angle_d1.4895844
X-RAY DIFFRACTIONf_dihedral_angle_d21.6422255
X-RAY DIFFRACTIONf_chiral_restr0.08636
X-RAY DIFFRACTIONf_plane_restr0.011494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7443-1.76550.2852510.29471380X-RAY DIFFRACTION32
1.7655-1.78790.3104720.30881972X-RAY DIFFRACTION46
1.7879-1.81140.2926970.29482791X-RAY DIFFRACTION66
1.8114-1.83620.3431140.28783314X-RAY DIFFRACTION79
1.8362-1.86240.26051410.27853818X-RAY DIFFRACTION86
1.8624-1.89020.26291350.26923740X-RAY DIFFRACTION89
1.8902-1.91980.26251410.26163967X-RAY DIFFRACTION91
1.9198-1.95120.30061460.24434045X-RAY DIFFRACTION93
1.9512-1.98490.251420.24433943X-RAY DIFFRACTION94
1.9849-2.0210.26321460.24074022X-RAY DIFFRACTION94
2.021-2.05980.25441480.23144127X-RAY DIFFRACTION95
2.0598-2.10190.28811460.22133977X-RAY DIFFRACTION95
2.1019-2.14750.25611480.20074149X-RAY DIFFRACTION96
2.1475-2.19750.19331440.18464001X-RAY DIFFRACTION95
2.1975-2.25240.24811520.18444150X-RAY DIFFRACTION96
2.2524-2.31330.23041460.17344036X-RAY DIFFRACTION95
2.3133-2.38130.17711480.17694094X-RAY DIFFRACTION96
2.3813-2.45820.19721500.18314143X-RAY DIFFRACTION97
2.4582-2.5460.21571500.18374191X-RAY DIFFRACTION96
2.546-2.64780.2361520.17844148X-RAY DIFFRACTION97
2.6478-2.76830.23681480.1834109X-RAY DIFFRACTION97
2.7683-2.91410.22751500.19784136X-RAY DIFFRACTION97
2.9141-3.09650.32391470.19414132X-RAY DIFFRACTION97
3.0965-3.33520.2411460.18334082X-RAY DIFFRACTION95
3.3352-3.67030.16161540.14464135X-RAY DIFFRACTION97
3.6703-4.20.14891490.1354124X-RAY DIFFRACTION96
4.2-5.28620.13761500.11744181X-RAY DIFFRACTION97
5.2862-28.93980.13731510.13454092X-RAY DIFFRACTION96
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)
12.8081-1.6544-1.34874.62914.23985.3858-0.05070.2533-0.1503-0.55150.3739-0.504-0.46140.9493-0.37970.4433-0.10680.07130.4329-0.03120.29613.7358-18.2625-23.3722
22.3167-2.71791.50347.9062-1.75252.80130.0626-0.0444-0.0335-0.82350.0040.7131-0.0022-0.1242-0.06890.3059-0.0016-0.06840.21140.01890.2518-17.955-25.5524-13.2481
32.70610.54672.20012.41722.27847.21670.2190.03-0.0885-0.0410.159-0.2020.51790.4988-0.34380.22140.0280.00840.22190.00060.2574-5.7477-40.0621-1.6047
47.7143-0.07290.00923.55312.60877.04530.0661-0.51920.72630.4977-0.02370.0435-0.0937-0.0564-0.03470.2068-0.00120.04430.3106-0.00050.2626-7.2798-31.6513.1996
57.861-4.18960.13146.97673.68473.62790.0959-0.6219-0.46580.2426-0.08410.5942-1.321-0.0698-0.04680.71060.00780.1220.52820.14640.4851-6.7668-13.8419-28.1851
62.64860.04370.46417.70361.47096.9160.17340.29520.1094-0.44420.54080.2770.7351-0.1653-0.73070.3764-0.05390.03210.38440.15420.344-7.6364-27.4657-17.2677
76.74335.0466-5.52015.5362-2.38166.83440.2465-0.38630.973-0.01050.15280.8018-0.2110.2357-0.4010.18130.0265-0.00390.27240.06830.3304-15.0982-28.74282.4513
80.53611.5285-0.37795.319-3.23013.7472-0.0067-0.1883-0.0487-0.2130.01690.12290.07990.159-0.00050.16110.02640.02760.24470.02230.1772-12.7234-28.271-3.4408
95.9877-2.23450.31228.63322.05974.24390.40870.3915-0.2843-0.49190.18320.3954-0.00690.5574-0.56790.4264-0.04170.04090.39940.0290.2916-2.3557-23.2358-24.7968
105.12922.91364.78052.0008-2.96778.31210.95140.75951.6274-1.054-0.23081.66840.16250.9105-0.7930.6771-0.06630.10050.79610.08820.5424-6.6304-16.0897-37.2381
113.4787-0.07340.73433.42763.21044.88110.0285-0.1943-0.25870.3685-0.30690.49130.648-0.35410.31940.4181-0.05880.08450.51140.02330.3388-8.5305-16.606236.5516
125.4617-2.718-2.07336.74973.25394.9430.0507-0.63140.1130.4870.0260.07310.057-0.0814-0.04510.2369-0.00970.00450.54790.07650.244114.1603-6.68836.4043
138.6010.67941.49456.90353.23312.5124-0.00820.0955-0.3716-0.49110.0890.05310.4920.0918-0.06190.3505-0.01690.03220.19290.04370.206412.1941-12.506315.3683
145.3254-1.05591.59258.04892.38716.59830.31320.088-0.0604-0.0594-0.34810.19710.2436-0.22620.02790.1731-0.0220.04420.26440.0230.2623.39186.7359.4789
156.01035.36877.04235.0326.45258.35960.1851-0.9371.46121.162-0.23971.993-0.0779-0.4630.0380.46620.01890.11680.3636-0.03280.61921.757820.815314.8208
161.5828-1.74222.52336.9060.78686.5588-0.6406-0.72390.75780.31160.157-0.2881-0.48930.88450.41880.6117-0.11340.04790.6890.11070.3955-0.1245-18.710844.6373
174.52543.5903-3.33824.7922-3.75512.96340.0007-0.3250.3949-0.1370.04080.27860.17150.2215-0.09290.21640.01050.02010.33570.00780.14559.6964-2.997622.7319
182.67660.23921.79364.769-3.9335.99480.1343-0.09830.0473-0.1525-0.0646-0.05030.16160.0057-0.09640.19170.00140.04360.25630.05460.231413.6082-0.215813.5746
194.6282.4174-1.59824.40230.34542.99650.00460.08250.02370.3738-0.04610.26880.4329-0.0590.08810.29690.02440.02990.37870.04410.18852.4313-12.237631.9386
205.855-3.60745.13658.5412-5.31196.74241.5216-1.56071.3851-0.0455-0.3121-0.91441.8426-0.0256-0.95170.818-0.15730.19160.7444-0.01390.52871.8111-27.009847.3473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 317 through 374 )
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 418 )
3X-RAY DIFFRACTION3chain 'A' and (resid 419 through 439 )
4X-RAY DIFFRACTION4chain 'A' and (resid 440 through 463 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 5 )
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 10 )
7X-RAY DIFFRACTION7chain 'B' and (resid 11 through 17 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 10 )
9X-RAY DIFFRACTION9chain 'C' and (resid 11 through 15 )
10X-RAY DIFFRACTION10chain 'C' and (resid 16 through 17 )
11X-RAY DIFFRACTION11chain 'D' and (resid 321 through 374 )
12X-RAY DIFFRACTION12chain 'D' and (resid 375 through 402 )
13X-RAY DIFFRACTION13chain 'D' and (resid 403 through 430 )
14X-RAY DIFFRACTION14chain 'D' and (resid 431 through 459 )
15X-RAY DIFFRACTION15chain 'D' and (resid 460 through 465 )
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 5 )
17X-RAY DIFFRACTION17chain 'E' and (resid 6 through 17 )
18X-RAY DIFFRACTION18chain 'F' and (resid 1 through 5 )
19X-RAY DIFFRACTION19chain 'F' and (resid 6 through 15 )
20X-RAY DIFFRACTION20chain 'F' and (resid 16 through 17 )

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