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- PDB-5k5l: Homo sapiens CCCTC-binding factor (CTCF) ZnF6-8 and H19 sequence ... -

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Basic information

Entry
Database: PDB / ID: 5k5l
TitleHomo sapiens CCCTC-binding factor (CTCF) ZnF6-8 and H19 sequence DNA complex structure
Components
  • DNA (5'-D(*GP*TP*TP*GP*CP*CP*GP*CP*GP*TP*G)-3')
  • DNA (5'-D(P*AP*CP*GP*CP*GP*GP*CP*AP*AP*C)-3')
  • Transcriptional repressor CTCF
KeywordsTRANSCRIPTION/DNA / CCCTC-binding factor / 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
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: 3.125 Å
AuthorsHashimoto, H. / 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
DepositionMay 23, 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: DNA (5'-D(*GP*TP*TP*GP*CP*CP*GP*CP*GP*TP*G)-3')
B: DNA (5'-D(P*AP*CP*GP*CP*GP*GP*CP*AP*AP*C)-3')
C: DNA (5'-D(*GP*TP*TP*GP*CP*CP*GP*CP*GP*TP*G)-3')
D: DNA (5'-D(P*AP*CP*GP*CP*GP*GP*CP*AP*AP*C)-3')
E: Transcriptional repressor CTCF
F: Transcriptional repressor CTCF
G: Transcriptional repressor CTCF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,58714
Polymers46,1307
Non-polymers4587
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-35 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.792, 52.397, 69.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: DNA chain DNA (5'-D(*GP*TP*TP*GP*CP*CP*GP*CP*GP*TP*G)-3')


Mass: 3381.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*GP*CP*GP*GP*CP*AP*AP*C)-3')


Mass: 3328.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein Transcriptional repressor CTCF / 11-zinc finger protein / CCCTC-binding factor / CTCFL paralog


Mass: 10903.598 Da / Num. of mol.: 3 / Fragment: unp residues 405-492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Plasmid: pXC1197 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL-codon plus / References: UniProt: P49711
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 20% (w/v) polyethylene glycol 8,000 0.1 M CHES-NaOH pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.2829 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 26, 2013
RadiationMonochromator: Si (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2829 Å / Relative weight: 1
ReflectionResolution: 3.125→46.725 Å / Num. obs: 15139 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 70.25 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.917
Reflection shellResolution: 3.125→3.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.556 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2313: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.125→46.725 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.49
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 756 4.99 %Random
Rwork0.2362 ---
obs0.2379 15139 96.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.125→46.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1642 856 7 2 2507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052670
X-RAY DIFFRACTIONf_angle_d0.5353718
X-RAY DIFFRACTIONf_dihedral_angle_d19.6731422
X-RAY DIFFRACTIONf_chiral_restr0.039393
X-RAY DIFFRACTIONf_plane_restr0.003329
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1255-3.23720.3705630.3326114177
3.2372-3.36680.3127730.2934142395
3.3668-3.51990.3259770.2708146998
3.5199-3.70540.3147810.2643146298
3.7054-3.93750.3213810.26221493100
3.9375-4.24130.2512770.2491485100
4.2413-4.66780.3046800.23371515100
4.6678-5.34240.272770.21611498100
5.3424-6.72760.2311770.2178148399
6.7276-46.70.2085700.1957141494
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)
15.76034.2461-4.07657.3747-5.21284.0190.52681.1759-0.8011-1.1930.41290.5844-0.2101-0.5093-0.73621.42670.1186-0.21891.2891-0.02750.7105144.263617.9628-13.1148
25.9264-0.80842.72844.82083.46594.36730.65981.5506-0.2714-0.74470.62460.20381.063-0.0331-1.13321.6305-0.2043-0.041.27350.16660.6611144.941117.3357-11.9992
35.1597-4.41071.53325.49871.44436.07840.317-1.23390.40671.03490.32090.1747-0.98390.7817-0.50021.1175-0.39190.14541.5947-0.00060.6288143.382717.410523.1053
44.0358-2.847-4.78766.8622.90338.45790.7895-1.16670.16840.9909-0.0745-0.2901-0.7748-0.9273-0.44310.9518-0.2181-0.03471.41290.0070.5825143.46217.139821.8367
57.74131.37670.74687.6693-3.40231.7565-0.28410.37070.06640.51760.5263-1.31661.4471-1.30790.18320.944-0.3728-0.06691.1994-0.12980.5201152.574932.3687-22.2442
61.57010.33260.46183.87960.55057.8097-0.32910.9137-0.0947-0.4814-0.11850.32720.9401-0.27330.41770.7595-0.0707-0.10530.9172-0.04630.4389142.600135.1647-9.3621
77.2022-0.0773.71623.15911.84348.29370.6026-0.6131-0.8830.9675-0.26750.1729-0.33690.309-0.44750.4106-0.2073-0.04150.55190.16020.8731130.89668.54116.7004
84.87860.9828-0.14323.1361-0.25934.96140.165-0.3223-3.07990.1038-0.4477-1.19180.80970.94290.08120.62810.0836-0.07840.88920.09521.2711128.23615.5763.8407
97.5913-5.52053.16076.421-6.64329.15080.40061.014-0.0232-2.31181.7033.1325-0.0764-3.07292.50170.8193-0.0122-0.22430.72470.44320.8296141.2718-4.4528-11.8544
105.913-5.60162.07387.3372-0.82341.3717-0.1974-0.980.92331.87031.06751.9666-0.7849-0.97190.05960.78350.17910.42990.68830.36811.2288145.22021.9732-4.8448
112.4253-0.9408-2.33364.0645-0.18917.25150.24-1.15030.14620.7664-0.24340.1816-0.35040.6025-0.14940.5889-0.17220.0170.7513-0.03630.2452160.612518.658113.647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:11)
2X-RAY DIFFRACTION2(chain B and resid 2:11)
3X-RAY DIFFRACTION3(chain C and resid 1:11)
4X-RAY DIFFRACTION4(chain D and resid 1:11)
5X-RAY DIFFRACTION5(chain E and resid 436:448)
6X-RAY DIFFRACTION6(chain E and resid 449:491)
7X-RAY DIFFRACTION7(chain F and resid 436:471)
8X-RAY DIFFRACTION8(chain F and resid 472:492)
9X-RAY DIFFRACTION9(chain G and resid 408:417)
10X-RAY DIFFRACTION10(chain G and resid 418:436)
11X-RAY DIFFRACTION11(chain G and resid 437:491)

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