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- PDB-5k5i: Homo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex s... -

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Basic information

Entry
Database: PDB / ID: 5k5i
TitleHomo sapiens CCCTC-binding factor (CTCF) ZnF5-8 and DNA complex structure in space group P65
Components
  • DNA (5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*GP*CP*AP*CP*C)-3')
  • DNA (5'-D(*GP*TP*GP*CP*CP*AP*GP*CP*AP*GP*GP*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 / genomic imprinting / protein localization to chromosome, centromeric region / 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 / genomic imprinting / protein localization to chromosome, centromeric region / 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 / male germ cell nucleus / epigenetic regulation of gene expression / transcription coregulator binding / 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 / sequence-specific DNA binding / in utero embryonic development / 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 / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...: / : / C2H2 zinc finger / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
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: 2.19 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 1.4Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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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*CP*TP*GP*CP*TP*GP*GP*CP*AP*CP*C)-3')
C: DNA (5'-D(*GP*TP*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0929
Polymers21,6693
Non-polymers4236
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-66 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.075, 45.075, 260.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 13722.850 Da / Num. of mol.: 1 / Fragment: unp residues 378-489
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Plasmid: pXC1199 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL-codon plus / References: UniProt: P49711

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*CP*CP*CP*TP*GP*CP*TP*GP*GP*CP*AP*CP*C)-3')


Mass: 3888.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*TP*GP*CP*CP*AP*GP*CP*AP*GP*GP*GP*G)-3')


Mass: 4057.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 16 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.52 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% (w/v) polyethylene glycol 3350, 0.2 M ammonium sulfate, 0.1 M sodium cacodylate 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: Feb 9, 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: 2.19→23.247 Å / Num. obs: 30205 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14.2 % / CC1/2: 0.806 / Rmerge(I) obs: 0.105 / Net I/σ(I): 19.29
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.333 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2400: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.19→23.247 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2447 1480 4.9 %RANDOM
Rwork0.2185 ---
obs0.2198 30205 96.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→23.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 527 10 10 1481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041572
X-RAY DIFFRACTIONf_angle_d0.4482197
X-RAY DIFFRACTIONf_dihedral_angle_d21.612614
X-RAY DIFFRACTIONf_chiral_restr0.031232
X-RAY DIFFRACTIONf_plane_restr0.003189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1726-2.24260.39651100.35532086X-RAY DIFFRACTION77
2.2426-2.32270.31751430.33872580X-RAY DIFFRACTION97
2.3227-2.41560.39161470.31722617X-RAY DIFFRACTION98
2.4156-2.52540.34331290.30432715X-RAY DIFFRACTION98
2.5254-2.65840.30381440.30382680X-RAY DIFFRACTION99
2.6584-2.82470.31981350.2872664X-RAY DIFFRACTION99
2.8247-3.04240.32481360.30962682X-RAY DIFFRACTION100
3.0424-3.34770.29781350.2532664X-RAY DIFFRACTION100
3.3477-3.83030.26741280.19792729X-RAY DIFFRACTION100
3.8303-4.81870.24131330.18362688X-RAY DIFFRACTION100
4.8187-23.24870.13371400.16022620X-RAY DIFFRACTION97

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