[English] 日本語
Yorodumi
- PDB-8sss: ZnFs 1-7 of CCCTC-binding factor (CTCF) Complexed with 23mer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sss
TitleZnFs 1-7 of CCCTC-binding factor (CTCF) Complexed with 23mer
Components
  • (DNA Strand (23mer) ...) x 2
  • Transcriptional repressor CTCF
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN / transcription factor / zinc fingers / insulator/chromatin architecture / transcription-dna complex / TRANSCRIPTION
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
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHorton, J.R. / Yang, J. / Cheng, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR160029 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structures of CTCF-DNA complexes including all 11 zinc fingers.
Authors: Yang, J. / Horton, J.R. / Liu, B. / Corces, V.G. / Blumenthal, R.M. / Zhang, X. / Cheng, X.
History
DepositionMay 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional repressor CTCF
B: DNA Strand (23mer) I
C: DNA Strand (23mer) II
D: Transcriptional repressor CTCF
E: DNA Strand (23mer) I
F: DNA Strand (23mer) II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,30322
Polymers76,3026
Non-polymers1,00116
Water1,910106
1
A: Transcriptional repressor CTCF
B: DNA Strand (23mer) I
C: DNA Strand (23mer) II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,69412
Polymers38,1513
Non-polymers5439
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Transcriptional repressor CTCF
E: DNA Strand (23mer) I
F: DNA Strand (23mer) II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,60910
Polymers38,1513
Non-polymers4587
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.013, 41.147, 135.661
Angle α, β, γ (deg.)90.000, 105.180, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 1 types, 2 molecules AD

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


Mass: 24023.834 Da / Num. of mol.: 2 / Fragment: Zinc finger domains 1-7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTCF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P49711

-
DNA Strand (23mer) ... , 2 types, 4 molecules BECF

#2: DNA chain DNA Strand (23mer) I


Mass: 6914.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA Strand (23mer) II


Mass: 7212.635 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 122 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 26.5% PEG3350, 0.26M DL-Malic acid 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→43.18 Å / Num. obs: 36617 / % possible obs: 94 % / Redundancy: 6 % / Biso Wilson estimate: 53.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Net I/σ(I): 17
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.989 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2757 / CC1/2: 0.513 / Rpim(I) all: 0.649 / % possible all: 74.4

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→43.18 Å / SU ML: 0.3407 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2311 1825 5 %
Rwork0.1989 34690 -
obs0.2005 36515 93.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.61 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 1874 19 106 5142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00285342
X-RAY DIFFRACTIONf_angle_d0.46467598
X-RAY DIFFRACTIONf_chiral_restr0.0325827
X-RAY DIFFRACTIONf_plane_restr0.0026649
X-RAY DIFFRACTIONf_dihedral_angle_d21.92322103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.35921010.33491910X-RAY DIFFRACTION68.54
2.36-2.430.3441190.32062271X-RAY DIFFRACTION79.51
2.43-2.510.37911260.34272395X-RAY DIFFRACTION86.1
2.51-2.60.37311450.33992748X-RAY DIFFRACTION96.34
2.6-2.70.31581470.28592787X-RAY DIFFRACTION99.12
2.7-2.820.31351470.27412809X-RAY DIFFRACTION99.43
2.82-2.970.32281500.26532836X-RAY DIFFRACTION99.24
2.97-3.160.32091490.27472836X-RAY DIFFRACTION99.37
3.16-3.40.22721440.20522742X-RAY DIFFRACTION96.91
3.4-3.740.20221440.17952738X-RAY DIFFRACTION95.08
3.74-4.280.20341480.16532820X-RAY DIFFRACTION99.53
4.29-5.40.1991530.15422893X-RAY DIFFRACTION99.51
5.4-43.180.15921520.14142905X-RAY DIFFRACTION96.37
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)
10.1731008759610.808054511043-0.5026771789147.96539067095-3.802332348022.123415584230.1758740946241.320390036981.218189987350.0825117786172-0.4499828561290.670765245066-1.167705998060.64267686730.1503090541221.089863692340.190224896153-0.0702721833521.353543241480.5365731319820.90687600876261.46383411798.397900320853.2834153705
22.6320206885-1.350648861932.696075272974.00972308433-5.08659297086.607863047930.225569669140.0829936831356-0.2436473329330.1135855113440.1799092087110.05146689104720.460841970871-0.0466172353477-0.4150630488330.4528830274950.096109747838-0.02939907174690.335943803118-0.02630224659820.37901631028269.0942914536-8.8670589851736.1173225391
30.6061963871150.3700334641231.473703416062.03988667097-0.2158206184213.73558142877-0.02839874512420.141963134077-0.1024029797510.09005459069880.0330227563332-0.0791766439509-0.00875366766770.260339728867-0.02389490894850.4225133309790.1392627105590.02287616566040.395419032969-0.04938106633310.36248862193469.3023099886-6.0200617832732.4804257663
44.303787976210.3231873594331.193891556277.54325684353-6.155132991627.450476863460.01496113087041.46561030961.11336559041-0.8812475986260.4313493467461.2052391149-1.36545512179-0.176303546696-0.4992639155841.180801631980.200629978504-0.04196882647631.129057695050.394293575010.79949424681758.97128477289.704519246180.355464242673
54.862555612820.420731375762-2.985063176843.260314293631.385273705088.109533804410.6346434653181.585050125390.205117600372-1.30208524665-0.204648082108-0.390196896455-0.752463263951-0.670315164494-0.4340602260790.9172882603520.253709080268-0.06197019956850.934189377069-0.08916969649290.74460003370427.38940003710.844631346718.8914902057
63.88407138351-0.5472983617460.5109033134692.3354107319-0.0813915358811.73504722810.0618639244097-0.0558658718599-0.615840115605-0.0271015069669-0.03111485894890.3844399434340.143492082893-0.270164214225-0.02630446970730.3873126815280.185392069262-0.0280470895090.63432945005-0.1280294918090.50336459681633.68798460132.1099588614239.3715339902
73.347413915660.831711802738-3.385356932632.14477626335-1.523592397147.639368188920.2981079585060.7995912367560.145656796448-0.0272918630312-0.2020112374260.318924838203-0.764578710452-1.18791026023-0.1230810026680.5419708955420.228011744798-0.06103346628250.530652889402-0.0881644250190.44151985529138.699839561519.998358307356.6170688476
82.09397321986-1.022662125590.8370854928741.751961875550.4966168224784.26122957289-0.0268788203304-0.650636895753-0.4543567992880.615860850597-0.298898311208-0.826722937942-0.04211373071820.2692379236280.329214892580.725549348595-0.00859037210563-0.09511487387410.3699452893920.1252995385920.82543971190652.64086086539.658721975.271152879
91.108453643571.055568876950.3455141355541.521067398692.01358020615.754818549140.2066584387330.0681821885528-0.140449674704-0.7981769503330.2682861605010.4810593029550.524438487544-0.6358214247450.4603784195911.31516738815-0.382331496356-0.418405930292.42725981264-1.50212085421.0422926440121.8307053835-2.8461681469421.7067985432
107.23366598936-4.21649550446-2.907559264332.744426071692.548206386263.667836334470.3153114227580.252658432655-0.560766453397-0.465175508034-0.166555998543-1.445915683980.627337586425-0.40133871107-0.1027059788310.7994235971770.0817378811072-0.1055580847590.851988942812-0.3959719326520.86167229261734.95364436965.8676026961331.2912965881
114.39414657860.778123332613-2.227977398460.773968376086-2.735864546279.954494127420.3877844358360.05506260468980.8063458749030.6424322223190.08287001164640.497697527703-1.16595674082-1.085836943640.2204469152960.6658821386390.209996351498-0.1089604628990.966752629051-0.5506923177730.77847090974334.060123542213.071651756848.4047342857
126.16343187186-0.504766442055-0.9488027992339.003885200636.239362220884.348391220730.483582663950.24220889118-0.1375734797270.0381709275550.0776830564775-1.44088255201-0.725000210757-0.2366218053-0.55386983150.772633551667-0.00630443575322-0.08849913570750.3495754871980.04095021338990.36195759989648.583042653317.760595913364.7943786512
131.817674823160.6827791422870.9657077174171.1667267086-0.05820216465052.286487899740.05704699265460.378609776181-0.2390820914290.145988028915-0.01585743525720.102645355404-0.37876403913-0.137656177586-0.03828556705250.5036180427090.158282491245-0.08788526993880.457737476825-0.09094302243970.39420289854840.838001753713.288095146155.7589034087
141.13755854282.00501006715-0.7165082203038.001921584124.05294898956.959515133610.2125244914320.921666023523-0.899745095312-1.65968461278-0.1194135552810.1017525109530.469883486273-0.857928481026-0.07267008516151.004213819660.0698420880334-0.2279895916791.17566245789-0.4468306471260.88954889029928.88166595540.77144649902923.0157551283
158.85550286392.463626788091.647829535313.08487058659-1.789501573054.355594067760.04406538442512.498069334820.727858480649-0.501532002163-0.03381769659651.19493686442-0.110272214012-0.254348140751-0.04252496002360.8357531855660.00193194184799-0.04878428359571.041284166090.1421771462670.71525209157556.3185601183-0.0362696886121-4.24310858704
165.72545477996-1.17622281836-0.5545385622396.569130046790.7050754055577.756588626620.3094896106030.8612594123140.84838645366-0.707871666371-0.0173575992434-0.761369641163-1.186224923630.568635429239-0.3004015123030.72082642601-0.105223567390.208732425890.7581925361690.01327706956050.48633392122374.97690043014.583007275815.64533667483
176.500640242390.449966036038-4.260391918063.12430481144-0.2884133350787.186288713570.2829200999850.1860195253780.69895925506-0.2736542717760.1251314983340.125688787235-1.06754217258-0.377273166786-0.4473426539330.5711268930110.191704712614-0.03317911622920.418636619155-0.1017271409560.43003872149859.93136912477.5078749656122.435375306
185.794691236881.486248790021.636330586262.971780485340.9820281077913.371176041860.009621337692090.882807416515-0.868862513903-0.157115417439-0.1117272053730.04703819287850.3861576398570.3279738875610.09676778492310.44690713780.1359367274210.005454486647840.432269729012-0.1343062815340.40767527532167.4139640288-14.479943564829.3656993664
194.945239493771.70476179132-1.123137519542.03191881964-0.2576900704895.979426444930.5274705641190.0453327139040.6975094464630.5756666927610.05911115505830.184008909546-0.3176025405540.44769628151-0.5728490000440.5820910478170.07339677498230.01607409938460.299381127753-0.008189335938540.53523791752176.2759392914-4.3247850162549.7730114623
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 1 through 10 )ES1 - 10
22chain 'E' and (resid 11 through 23 )ES11 - 23
33chain 'F' and (resid 1 through 15 )FT1 - 15
44chain 'F' and (resid 16 through 23 )FT16 - 23
55chain 'A' and (resid 265 through 305 )AA265 - 3051 - 41
66chain 'A' and (resid 306 through 374 )AA306 - 37442 - 110
77chain 'A' and (resid 375 through 430 )AA375 - 430111 - 166
88chain 'A' and (resid 431 through 461 )AA431 - 461167 - 197
99chain 'B' and (resid 1 through 5 )BI1 - 5
1010chain 'B' and (resid 6 through 10 )BI6 - 10
1111chain 'B' and (resid 11 through 15 )BI11 - 15
1212chain 'B' and (resid 16 through 23 )BI16 - 23
1313chain 'C' and (resid 1 through 15 )CJ1 - 15
1414chain 'C' and (resid 16 through 23 )CJ16 - 23
1515chain 'D' and (resid 265 through 305 )DK265 - 3051 - 41
1616chain 'D' and (resid 306 through 333 )DK306 - 33342 - 69
1717chain 'D' and (resid 334 through 374 )DK334 - 37470 - 110
1818chain 'D' and (resid 375 through 418 )DK375 - 418111 - 154
1919chain 'D' and (resid 419 through 462 )DK419 - 462155 - 198

+
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://pdbjlvh1.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