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- PDB-5t0u: CTCF ZnF2-7 and DNA complex structure -

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Basic information

Entry
Database: PDB / ID: 5t0u
TitleCTCF ZnF2-7 and DNA complex structure
Components
  • DNA (5'-D(*CP*CP*TP*CP*AP*CP*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3')
  • DNA (5'-D(*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*CP*TP*AP*GP*TP*GP*AP*GP*G)-3')
  • Transcriptional repressor CTCF
KeywordsTRANSCRIPTION REGULATOR/DNA / CCCTC-binding factor / CTCF / zinc finger / TRANSCRIPTION REGULATOR-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 / chromosome segregation / transcription coregulator binding / 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: 3.199 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
DepositionAug 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 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 27, 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(*CP*CP*TP*CP*AP*CP*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*AP*GP*TP*GP*AP*GP*G)-3')
D: Transcriptional repressor CTCF
E: DNA (5'-D(*CP*CP*TP*CP*AP*CP*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*AP*GP*TP*GP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,47918
Polymers69,6946
Non-polymers78512
Water21612
1
A: Transcriptional repressor CTCF
B: DNA (5'-D(*CP*CP*TP*CP*AP*CP*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*AP*GP*TP*GP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2409
Polymers34,8473
Non-polymers3926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-56 kcal/mol
Surface area15800 Å2
MethodPISA
2
D: Transcriptional repressor CTCF
E: DNA (5'-D(*CP*CP*TP*CP*AP*CP*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*AP*GP*TP*GP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2409
Polymers34,8473
Non-polymers3926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-60 kcal/mol
Surface area16180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.630, 40.960, 106.670
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number3
Space group name H-MP121

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Components

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


Mass: 20720.023 Da / Num. of mol.: 2 / Fragment: UNP residues 294-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Plasmid: pXC1565 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus / References: UniProt: P49711
#2: DNA chain DNA (5'-D(*CP*CP*TP*CP*AP*CP*TP*AP*GP*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*GP*C)-3')


Mass: 6914.437 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*AP*GP*TP*GP*AP*GP*G)-3')


Mass: 7212.635 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.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 15% PEG 4000, 0.2 M ammonium acetate, 0.2 M Na-Citrate pH 5.6

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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: Jul 2, 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: 3.19→53.4 Å / Num. obs: 27870 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 8.2
Reflection shellResolution: 3.19→3.28 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.34 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX(1.11_2558: ???)refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.199→53.295 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2663 1393 5.04 %Random
Rwork0.2297 ---
obs0.2314 27648 97.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.199→53.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 1874 12 12 4663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054987
X-RAY DIFFRACTIONf_angle_d0.527044
X-RAY DIFFRACTIONf_dihedral_angle_d19.1912624
X-RAY DIFFRACTIONf_chiral_restr0.037764
X-RAY DIFFRACTIONf_plane_restr0.002575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1994-3.31370.42181290.34872403X-RAY DIFFRACTION90
3.3137-3.44640.31861420.30912607X-RAY DIFFRACTION96
3.4464-3.60320.31491230.27992575X-RAY DIFFRACTION97
3.6032-3.79310.33641420.26942696X-RAY DIFFRACTION98
3.7931-4.03070.25761400.24932636X-RAY DIFFRACTION99
4.0307-4.34180.23591510.21992643X-RAY DIFFRACTION99
4.3418-4.77850.25831530.20422682X-RAY DIFFRACTION99
4.7785-5.46930.25811290.20332684X-RAY DIFFRACTION100
5.4693-6.88840.22271450.20462713X-RAY DIFFRACTION99
6.8884-53.30260.22031390.17572616X-RAY DIFFRACTION97
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)
12.57420.34970.78430.4940.77830.70990.23420.1855-0.15680.1099-0.1161-0.20180.0889-0.19410.0070.55310.1189-0.110.5251-0.0270.662412.53859.301440.6172
20.47820.0354-0.62220.8569-0.14011.0312-0.29640.2757-0.5648-0.30110.3381-0.3237-0.3737-0.61430.22930.60590.0288-0.00850.7198-0.11870.69719.4459.79235.3842
30.533-0.5391-0.67520.4101-0.14250.82450.18950.307-0.4665-0.0942-0.02540.0004-0.0012-0.39570.02360.54740.1142-0.05250.6431-0.06460.56918.43828.713734.344
40.0044-0.006-0.01660.00420.03030.0224-0.84040.1732-0.0861-0.217-0.5109-0.24930.1111-0.5065-01.60950.39350.01322.2519-0.53041.441936.6786-9.4251-5.0024
50.00650.0049-0.00030.0024-0.00230.00690.15910.1729-0.1339-0.0460.0834-0.056-0.0971-0.015-0.00011.9442-0.1388-0.7813.41740.15971.926444.6869-5.6662-2.4574
61.3319-0.29420.71691.6694-0.51720.75750.27820.5423-0.11580.2398-0.13250.06320.0589-0.0532-0.00380.73640.25330.02070.7693-0.09930.575348.8535-4.527427.4761
70.3396-1.38370.23775.2031-1.18682.18060.09961.24-0.6764-0.14430.96620.9849-0.72230.11570.88670.90110.1041-0.11781.98350.13040.6928.76911.86852.0497
80.4813-0.4435-0.01950.3116-0.08260.0172-0.11490.5959-0.54220.24150.33170.3306-0.8296-0.461-0.01311.00720.2479-0.17620.9513-0.00570.791250.296-10.197430.3515
90.4701-0.27-0.41560.4234-0.01390.2430.25651.1236-0.5158-0.0624-0.13530.0945-0.05880.1906-0.00980.87190.2404-0.1620.8512-0.17430.673950.5464-7.801829.4344
100.22350.36810.03770.7418-0.37390.767-0.24011.52610.68420.18390.27010.2483-1.37010.5870.00021.31350.4426-0.11661.95780.01560.834226.79740.37551.369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 293:462)
2X-RAY DIFFRACTION2(chain B and resid 1:23)
3X-RAY DIFFRACTION3(chain C and resid 1:23)
4X-RAY DIFFRACTION4(chain D and resid 294:311)
5X-RAY DIFFRACTION5(chain D and resid 312:317)
6X-RAY DIFFRACTION6(chain D and resid 318:462)
7X-RAY DIFFRACTION7(chain E and resid 1:9)
8X-RAY DIFFRACTION8(chain E and resid 10:23)
9X-RAY DIFFRACTION9(chain F and resid 1:14)
10X-RAY DIFFRACTION10(chain F and resid 15:23)

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