[English] 日本語
Yorodumi
- PDB-8sst: ZnFs 1-7 of CCCTC-binding factor (CTCF) K365T Mutant Complexed wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sst
TitleZnFs 1-7 of CCCTC-binding factor (CTCF) K365T Mutant 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 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 / 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: 2.19 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)77,41024
Polymers76,2466
Non-polymers1,16418
Water1,892105
1
A: Transcriptional repressor CTCF
B: DNA Strand (23mer) I
C: DNA Strand (23mer) II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,76713
Polymers38,1233
Non-polymers64410
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)38,64311
Polymers38,1233
Non-polymers5208
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)160.561, 41.596, 135.215
Angle α, β, γ (deg.)90.000, 105.610, 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: 23995.758 Da / Num. of mol.: 2 / Fragment: Zinc finger domains 1-7 / Mutation: K365T
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): CodonPlus / 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 , 3 types, 123 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.85 Å3/Da / Density % sol: 56.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

-
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: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→40.17 Å / Num. obs: 43468 / % possible obs: 97.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 50.72 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.053 / Net I/σ(I): 13.3
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.315 / Mean I/σ(I) obs: 1 / Num. unique obs: 3842 / CC1/2: 0.387 / Rsym value: 0.753 / % possible all: 87.4

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→40.17 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2434 1991 4.6 %
Rwork0.2203 41322 -
obs0.2214 43313 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.23 Å2
Refinement stepCycle: LAST / Resolution: 2.19→40.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 1874 30 105 5149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295337
X-RAY DIFFRACTIONf_angle_d0.4657586
X-RAY DIFFRACTIONf_chiral_restr0.0319827
X-RAY DIFFRACTIONf_plane_restr0.0031648
X-RAY DIFFRACTIONf_dihedral_angle_d21.63592096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.250.36941200.34752490X-RAY DIFFRACTION83.07
2.25-2.310.35451350.32622840X-RAY DIFFRACTION92.45
2.31-2.380.3911360.32892840X-RAY DIFFRACTION95.85
2.38-2.450.33171430.33452968X-RAY DIFFRACTION97.62
2.45-2.540.35091400.32492906X-RAY DIFFRACTION97.01
2.54-2.640.37231460.31123021X-RAY DIFFRACTION99.5
2.64-2.760.29851470.28763055X-RAY DIFFRACTION99.66
2.76-2.910.28491440.28142993X-RAY DIFFRACTION99.49
2.91-3.090.29631460.27973030X-RAY DIFFRACTION99.37
3.09-3.330.24471430.24162933X-RAY DIFFRACTION96.61
3.33-3.670.19771420.20212942X-RAY DIFFRACTION95.87
3.67-4.20.23791480.19453088X-RAY DIFFRACTION99.94
4.2-5.280.19821500.17643090X-RAY DIFFRACTION99.85
5.29-40.170.19481510.16073126X-RAY DIFFRACTION97.18
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)
18.18286441286-0.120284562522-2.434717822315.95210652717-0.06370830607455.066683251980.4058636985251.363775779690.538730113939-0.4583641748180.374822010698-0.0593387907924-1.222144279860.00567998972312-0.6664294273130.9378954840470.02575384955150.2673895930350.9086642826710.03655956233510.53811864432270.91198746162.871324095544.91161083201
24.006356712560.460612752955-0.5245197544362.099456998350.4814651616255.880558292770.3720737751890.529887367648-0.0717543673977-0.254904581305-0.3758744995080.227776690698-0.313090294239-0.204829352683-0.02849768686060.4928521165560.197572649848-0.004999547053220.555833398311-0.1615779665240.39218071265364.5941573001-6.3395449233928.8855684524
38.254058960810.350262487758-0.9344398575287.274265740012.651015585722.547181681880.449712664833-0.2928870014430.7181423674830.647422833986-0.1210595571780.185615503128-0.4011048116370.320843968329-0.3599911551240.5919292142060.01942474760460.02100967603530.304579651098-0.04505060186180.44749991932274.1868228136-3.1887804647153.6997679148
40.8487693813812.06552064909-2.115784511399.35006327089-4.921055370952.141492991510.970669438351.713656744691.68051085640.289240543543-0.7433722020021.12311171731-1.655425431790.038842401422-0.2115887486011.374927717890.515523578240.05524507279282.303993696110.9509014530221.0879760600661.4676366317.867944647712.54284227555
53.19398390304-2.351070204912.554931331016.99161658984-6.78036766142.642958283680.1884066639620.485219953913-0.2481514056670.2003339077770.2243959174660.09574746756010.6322279096630.374046845634-0.4072155299750.5278063970320.0578324499758-0.07669462776280.391368863567-0.06975032143850.35142778214868.2801988741-8.925981321135.9131918059
60.1828290624360.593096650651.068454430380.5814949793871.075569035968.27103188890.1455719919910.263236816499-0.1211753327560.014411260729-0.002222145663330.0884010824019-0.448065126650.213897590271-0.1582938358720.4532473359610.1589718101370.009498003531720.406326808728-0.05980176660050.39430440118768.5807556101-6.020852494832.368200206
77.34583263673-0.2442618080211.051184626969.04108347297-3.035778937823.307049839780.6033923275932.037770496391.8048740194-1.474095770961.305957578331.89281407662-1.47228884726-1.85735301469-1.689887331241.616718806310.5985939704950.3156816421712.248740732650.7338892674631.1207432561359.40121984449.79557443618-0.740319768316
86.47334085187-1.18254563745-7.060259859590.3267440220450.795326534489.987545710130.6823023686092.09763981012-0.699077653391-2.121139586790.0195638221794-2.73557892730.5711731565742.32690122572-0.72551819611.71285661240.008095797205640.4692585544922.46028754311-0.6365210853931.6220240276932.12523099515.6645985971712.3455888055
95.458075103411.77424681134-5.165207664755.85185585656-1.488525351217.980809168030.5324659142843.251818823671.80790563509-1.01288943341-0.1474676714020.041800283357-1.02951118187-1.77371026055-0.3855499715270.8371607760220.389922477288-0.1214761719931.545320292190.1284787813631.0201469884518.610050224416.163397792725.1371862894
103.55280217130.6302146373470.8211597708141.87378614958-0.1499123536841.767175976650.4097084797080.64403898165-0.531601460062-0.120015967466-0.1730964071940.1181596621420.197298824597-0.228971050704-0.2352758574610.487904882760.254313014364-0.05395404941640.739820729239-0.2080435117520.57998847108233.02437165172.024366020238.9995690977
113.36234762136-0.461700320691-0.2520401924054.09554507659-3.038735972317.35871934430.04880246272890.227017609443-0.2242483156990.0690836738008-0.19698938751-0.0394343601915-0.171671164773-0.4424182246870.1223246136490.4629591214280.0685969415517-0.003373311895440.218812438722-0.1308726303950.44760348904342.708682562716.686118500262.4453829301
120.6159200945820.51949489201-0.2554172930732.63448606792.63435698033.864748739420.632584744007-0.200084117978-0.201361049643-0.9218403795590.6906761759360.438599572845-0.161749751327-0.684791924852-0.2378744524271.59074594674-0.525046020049-0.6919599090463.24169479946-2.428387808751.591488931620.3459669384-2.2350894536421.765354322
135.71575013644-1.41087445180.09351146852664.2752258514-4.398242136452.281102712020.02966820062150.74929791698-0.119670238444-0.275456521276-0.1065428225070.21303996268-0.117588043047-0.8188968710640.1151376325360.6300819290160.13225589188-0.1258792547090.852368867381-0.4006866846290.84191044436733.9188809519.1591174926838.909635087
146.62133476954-0.966136602252-0.5353327404692.285538195718.960770782637.210723190330.6518137352960.157551091565-0.432588716858-0.2344803340180.0488255310988-1.35725465877-0.439807942342-0.0457983962602-0.6214066200050.8128927938890.0365014880546-0.09439527779150.2683645039640.05741284879010.41068813412947.822948097417.997566338364.3534765915
153.45780212137-1.38852990139-1.571479567376.06722123680.7317359020259.012001296330.3746343894370.551800564532-0.194801275129-0.220616768666-0.3937917694660.0708052352238-0.707218574723-0.745382398235-0.01742629053970.4170883644990.107848181867-0.04114839756230.329697292075-0.04970795476080.34579385217444.636211761716.920458230761.2745939916
161.047470041360.5908548415590.9031324609661.37234659141-1.099776456522.86188074382-0.0873641676022-0.4370393784510.153568451680.1724736126480.1844289757960.25310176672-0.0605767767588-0.4417162346480.03567287818380.527238735340.322807102664-0.06063070116820.776951048801-0.2156799194650.53618283722831.46661557396.4014671515843.2907946237
175.34950972865-6.69770937288-6.138203527842.107183692056.880145983387.249994996710.5303280296793.20201017606-1.26482257747-2.064911435010.775077078866-0.3861355689430.845098480048-0.22613132699-0.859461989581.092551776480.195638232869-0.05315350727662.05048179977-0.8988956570841.2704120622628.64847788195.9993881620624.810498475
181.999395745221.66010332596.791743617062.036543627672.509235422018.2743185515-1.431116446811.45673392789-2.63418487194-0.381331132045-1.286752838992.019170990481.85336407139-3.725223056022.111336746382.12355840897-0.509779087156-0.03725469976022.70838571862-1.232581481312.1204666348624.750247059-8.916009848219.2940226079
192.01912522803-0.751255699939-2.343844329270.06689497256850.3854002335692.003500099922.398049488422.69955001531.39863357736-0.801834570704-0.5336277993662.04374025509-0.6903033283390.379533777585-1.927835373171.583031318310.1908116899350.07550109682432.480015743970.7250367151211.9350900033748.15615604415.28930960419-5.3648671937
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 289 through 344 )DN289 - 34425 - 80
22chain 'D' and (resid 345 through 429 )DN345 - 42981 - 165
33chain 'D' and (resid 430 through 462 )DN430 - 462166 - 198
44chain 'E' and (resid 1 through 10 )EV1 - 10
55chain 'E' and (resid 11 through 23 )EV11 - 23
66chain 'F' and (resid 1 through 15 )FW1 - 15
77chain 'F' and (resid 16 through 23 )FW16 - 23
88chain 'A' and (resid 265 through 287 )AA265 - 2871 - 23
99chain 'A' and (resid 288 through 305 )AA288 - 30524 - 41
1010chain 'A' and (resid 306 through 374 )AA306 - 37442 - 110
1111chain 'A' and (resid 375 through 461 )AA375 - 461111 - 197
1212chain 'B' and (resid 1 through 5 )BJ1 - 5
1313chain 'B' and (resid 6 through 15 )BJ6 - 15
1414chain 'B' and (resid 16 through 23 )BJ16 - 23
1515chain 'C' and (resid 1 through 10 )CK1 - 10
1616chain 'C' and (resid 11 through 15 )CK11 - 15
1717chain 'C' and (resid 16 through 20 )CK16 - 20
1818chain 'C' and (resid 21 through 23 )CK21 - 23
1919chain 'D' and (resid 265 through 288 )DN265 - 2881 - 24

+
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