[English] 日本語
Yorodumi
- PDB-5kkq: Homo sapiens CCCTC-binding factor (CTCF) ZnF3-7 and DNA complex s... -

+
Open data


ID or keywords:

Loading...

-
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 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 / 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 / : / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more