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- PDB-5k5h: Homo sapiens CCCTC-binding factor (CTCF) ZnF4-7 and DNA complex s... -

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Basic information

Entry
Database: PDB / ID: 5k5h
TitleHomo sapiens CCCTC-binding factor (CTCF) ZnF4-7 and DNA complex structure
Components
  • DNA (5'-D(*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*C)-3')
  • DNA (5'-D(*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*G)-3')
  • Transcriptional repressor CTCF
KeywordsTRANSCRIPTION/DNA / CCCTC-binding factor / CTCF / zinc finger / TRANSCRIPTION-DNA complex
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 / in utero embryonic development / 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 / 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 / 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: 3.108 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: Transcriptional repressor CTCF
B: DNA (5'-D(*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*C)-3')
C: DNA (5'-D(*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4097
Polymers22,1483
Non-polymers2624
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-24 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.800, 52.800, 166.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 14200.445 Da / Num. of mol.: 1 / Fragment: unp residues 348-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Plasmid: pXC1202 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL-codon plus / References: UniProt: P49711
#2: DNA chain DNA (5'-D(*CP*AP*GP*CP*AP*GP*GP*GP*GP*GP*CP*GP*C)-3')


Mass: 4042.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*CP*CP*CP*CP*CP*TP*GP*CP*TP*GP*G)-3')


Mass: 3904.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% (w/v) polyethylene glycol 3350, 0.2 M ammonium acetate, 0.1 M bis-tris HCl, pH 5.5

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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: Feb 26, 2015
RadiationMonochromator: Si (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27046 Å / Relative weight: 1
ReflectionResolution: 3.108→50.321 Å / Num. obs: 44172 / % possible obs: 70.8 % / Observed criterion σ(F): 3 / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.56
Reflection shellResolution: 3.108→3.19 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.059 / % possible all: 4.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2400: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.108→50.321 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.61
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 340 10.04 %RANDOM
Rwork0.2365 ---
obs0.2395 44172 72.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.108→50.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 527 4 7 1444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041535
X-RAY DIFFRACTIONf_angle_d0.4542149
X-RAY DIFFRACTIONf_dihedral_angle_d23.758607
X-RAY DIFFRACTIONf_chiral_restr0.031231
X-RAY DIFFRACTIONf_plane_restr0.002182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.108-3.91550.30241060.2533855X-RAY DIFFRACTION43
3.9155-50.32740.2492340.22992190X-RAY DIFFRACTION100
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)
12.6528-1.7544-2.84534.32721.16226.348-0.6613-0.27850.958-0.16160.911-0.3226-1.66321.9372-0.02320.923-0.1363-0.09390.5574-0.010.5064-20.540818.65193.674
27.2985-6.2091-3.47295.41373.51894.07090.35140.08430.11330.61390.55360.42190.9419-0.1157-0.70870.7461-0.23360.03511.0546-0.25751.7809-6.996412.2671-1.4934
31.87-0.7990.86552.03650.5772.18910.1816-0.31450.15110.25310.4016-0.2950.06710.18090.03890.22020.14160.13740.8967-0.17530.3091-16.7019-5.6657-6.8054
40.1142-0.1420.01432.5113-0.15630.34730.24080.86680.4771-0.8703-0.3270.93810.65940.43280.06671.0063-0.4875-0.3481.6830.05161.1299-36.3813-10.0842-17.0542
51.00570.7337-2.53968.0986-1.66716.41391.06530.64121.4658-1.0307-0.08710.7865-0.7339-1.3184-0.8910.46410.12730.2271.10240.02820.7428-30.10216.3118-25.4887
61.7417-0.707-1.57251.68851.96883.90890.23050.16340.0702-0.20460.2224-0.0947-0.52170.3878-0.3040.31580.070.10240.6203-0.09610.236-21.14452.9108-3.2958
70.7136-1.2476-2.23863.30013.5927.11470.25790.54140.1767-0.6038-0.1021-0.3077-0.97730.5504-0.2650.34880.14560.02140.9573-0.05220.3265-19.81572.6132-7.6292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 350 through 371 )
2X-RAY DIFFRACTION2chain 'A' and (resid 372 through 381 )
3X-RAY DIFFRACTION3chain 'A' and (resid 382 through 429 )
4X-RAY DIFFRACTION4chain 'A' and (resid 430 through 434 )
5X-RAY DIFFRACTION5chain 'A' and (resid 435 through 460 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 13 )
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 15 )

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