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- EMDB-32252: Cryo-EM structure of human cohesin-CTCF-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32252
TitleCryo-EM structure of human cohesin-CTCF-DNA complex
Map data
Sample
  • Complex: Human cohesin-NIPBL-CTCF-DNA complex
    • Complex: Human cohesin-NIPBL-CTCF
      • Protein or peptide: x 6 types
    • Complex: DNA
      • DNA: x 2 types
  • Ligand: x 3 types
KeywordsCohesin / NIPBL / CTCF / DNA / chromosome folding / topologically associating domain / chromatin loops / DNA loop extrusion / sister chromatid cohesion / complex / ATPase / HEAT repeat protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / chromatin loop anchoring activity / regulation of hair cycle / response to DNA damage checkpoint signaling / chromatin insulator sequence binding ...eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / chromatin loop anchoring activity / regulation of hair cycle / response to DNA damage checkpoint signaling / chromatin insulator sequence binding / forelimb morphogenesis / maintenance of mitotic sister chromatid cohesion / negative regulation of mitotic metaphase/anaphase transition / embryonic viscerocranium morphogenesis / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / positive regulation of sister chromatid cohesion / mitotic cohesin complex / uterus morphogenesis / regulation of centromeric sister chromatid cohesion / negative regulation of G2/M transition of mitotic cell cycle / establishment of protein localization to chromatin / regulation of developmental growth / negative regulation of glial cell apoptotic process / genomic imprinting / embryonic digestive tract morphogenesis / cellular response to X-ray / positive regulation of neuron migration / chromo shadow domain binding / lateral element / replication-born double-strand break repair via sister chromatid exchange / mediator complex binding / protein localization to chromosome, centromeric region / integrator complex / establishment of mitotic sister chromatid cohesion / positive regulation of multicellular organism growth / metanephros development / chromatin looping / positive regulation of ossification / embryonic forelimb morphogenesis / reciprocal meiotic recombination / digestive tract development / cardiac muscle cell development / face morphogenesis / microtubule motor activity / sister chromatid cohesion / negative regulation of interleukin-1 beta production / mitotic sister chromatid cohesion / stem cell population maintenance / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / lncRNA binding / mitotic spindle pole / dynein complex binding / beta-tubulin binding / fat cell differentiation / outflow tract morphogenesis / regulation of DNA replication / mitotic sister chromatid segregation / regulation of embryonic development / positive regulation of interleukin-10 production / somatic stem cell population maintenance / negative regulation of tumor necrosis factor production / chromosome, centromeric region / mitotic spindle assembly / developmental growth / SUMOylation of DNA damage response and repair proteins / heart morphogenesis / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / condensed chromosome / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / male germ cell nucleus / epigenetic regulation of gene expression / transcription coregulator binding / condensed nuclear chromosome / meiotic cell cycle / mitochondrion organization / chromosome segregation / promoter-specific chromatin binding / sensory perception of sound / response to radiation / brain development / kinetochore / DNA-binding transcription repressor activity, RNA polymerase II-specific / cognition / nuclear matrix / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle pole / transcription corepressor activity / sequence-specific double-stranded DNA binding / Separation of Sister Chromatids / protein localization / double-strand break repair / mitotic cell cycle
Similarity search - Function
HEAT repeat associated with sister chromatid cohesion protein / Sister chromatid cohesion C-terminal domain / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / : / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA ...HEAT repeat associated with sister chromatid cohesion protein / Sister chromatid cohesion C-terminal domain / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / : / Cohesin subunit SCC3/SA, HEAT-repeats domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative domain / Stromalin conservative (SCD) domain profile. / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / : / : / C2H2 zinc finger / Smc1, ATP-binding cassette domain / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal 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 / Armadillo-like helical / Armadillo-type fold / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Double-strand-break repair protein rad21 homolog / Transcriptional repressor CTCF / Structural maintenance of chromosomes protein 1A / Nipped-B-like protein / Cohesin subunit SA-1 / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsShi ZB / Bai XC
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124096, GM143158, GM136976 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP160667-P2, RP160082 United States
Welch FoundationI-1441, I-1944 United States
CitationJournal: Mol Cell / Year: 2023
Title: CTCF and R-loops are boundaries of cohesin-mediated DNA looping.
Authors: Hongshan Zhang / Zhubing Shi / Edward J Banigan / Yoori Kim / Hongtao Yu / Xiao-Chen Bai / Ilya J Finkelstein /
Abstract: Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, ...Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, we present direct evidence that CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging, we demonstrate that a critical N-terminal motif of CTCF blocks cohesin translocation and DNA looping. The cryo-EM structure of the cohesin-CTCF complex reveals that this CTCF motif ahead of zinc fingers can only reach its binding site on the STAG1 cohesin subunit when the N terminus of CTCF faces cohesin. Remarkably, a C-terminally oriented CTCF accelerates DNA compaction by cohesin. DNA-bound Cas9 and Cas12a ribonucleoproteins are also polar cohesin barriers, indicating that stalling may be intrinsic to cohesin itself. Finally, we show that RNA-DNA hybrids (R-loops) block cohesin-mediated DNA compaction in vitro and are enriched with cohesin subunits in vivo, likely forming TAD boundaries.
History
DepositionNov 19, 2021-
Header (metadata) releaseMay 31, 2023-
Map releaseMay 31, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32252.png

Downloads & links

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Map

FileDownload / File: emd_32252.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 360 pix.
= 518.4 Å		1.44 Å/pix.
x 360 pix.
= 518.4 Å		1.44 Å/pix.
x 360 pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.12225401 - 0.22339071
Average (Standard dev.)0.000029603441 (±0.003944391)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 518.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human cohesin-NIPBL-CTCF-DNA complex

EntireName: Human cohesin-NIPBL-CTCF-DNA complex
Components
  • Complex: Human cohesin-NIPBL-CTCF-DNA complex
    • Complex: Human cohesin-NIPBL-CTCF
      • Protein or peptide: Structural maintenance of chromosomes protein 1A
      • Protein or peptide: Structural maintenance of chromosomes protein 3
      • Protein or peptide: Double-strand-break repair protein rad21 homolog
      • Protein or peptide: Cohesin subunit SA-1
      • Protein or peptide: Nipped-B-like protein
      • Protein or peptide: Transcriptional repressor CTCF
    • Complex: DNA
      • DNA: DNA (118-MER)
      • DNA: DNA (118-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: ZINC ION

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Supramolecule #1: Human cohesin-NIPBL-CTCF-DNA complex

SupramoleculeName: Human cohesin-NIPBL-CTCF-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Human cohesin-NIPBL-CTCF

SupramoleculeName: Human cohesin-NIPBL-CTCF / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5, #8

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6-#7

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Macromolecule #1: Structural maintenance of chromosomes protein 1A

MacromoleculeName: Structural maintenance of chromosomes protein 1A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 143.485094 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGFLKLIEIE NFKSYKGRQI IGPFQRFTAI IGPNGSGKSN LMDAISFVLG EKTSNLRVKT LRDLIHGAPV GKPAANRAFV SMVYSEEGA EDRTFARVIV GGSSEYKINN KVVQLHEYSE ELEKLGILIK ARNFLVFQGA VESIAMKNPK ERTALFEEIS R SGELAQEY ...String:
MGFLKLIEIE NFKSYKGRQI IGPFQRFTAI IGPNGSGKSN LMDAISFVLG EKTSNLRVKT LRDLIHGAPV GKPAANRAFV SMVYSEEGA EDRTFARVIV GGSSEYKINN KVVQLHEYSE ELEKLGILIK ARNFLVFQGA VESIAMKNPK ERTALFEEIS R SGELAQEY DKRKKEMVKA EEDTQFNYHR KKNIAAERKE AKQEKEEADR YQRLKDEVVR AQVQLQLFKL YHNEVEIEKL NK ELASKNK EIEKDKKRMD KVEDELKEKK KELGKMMREQ QQIEKEIKEK DSELNQKRPQ YIKAKENTSH KIKKLEAAKK SLQ NAQKHY KKRKGDMDEL EKEMLSVEKA RQEFEERMEE ESQSQGRDLT LEENQVKKYH RLKEEASKRA ATLAQELEKF NRDQ KADQD RLDLEERKKV ETEAKIKQKL REIEENQKRI EKLEEYITTS KQSLEEQKKL EGELTEEVEM AKRRIDEINK ELNQV MEQL GDARIDRQES SRQQRKAEIM ESIKRLYPGS VYGRLIDLCQ PTQKKYQIAV TKVLGKNMDA IIVDSEKTGR DCIQYI KEQ RGEPETFLPL DYLEVKPTDE KLRELKGAKL VIDVIRYEPP HIKKALQYAC GNALVCDNVE DARRIAFGGH QRHKTVA LD GTLFQKSGVI SGGASDLKAK ARRWDEKAVD KLKEKKERLT EELKEQMKAK RKEAELRQVQ SQAHGLQMRL KYSQSDLE Q TKTRHLALNL QEKSKLESEL ANFGPRINDI KRIIQSRERE MKDLKEKMNQ VEDEVFEEFC REIGVRNIRE FEEEKVKRQ NEIAKKRLEF ENQKTRLGIQ LDFEKNQLKE DQDKVHMWEQ TVKKDENEIE KLKKEEQRHM KIIDETMAQL QDLKNQHLAK KSEVNDKNH EMEEIRKKLG GANKEMTHLQ KEVTAIETKL EQKRSDRHNL LQACKMQDIK LPLSKGTMDD ISQEEGSSQG E DSVSGSQR ISSIYAREAL IEIDYGDLCE DLKDAQAEEE IKQEMNTLQQ KLNEQQSVLQ RIAAPNMKAM EKLESVRDKF QE TSDEFEA ARKRAKKAKQ AFEQIKKERF DRFNACFESV ATNIDEIYKA LSRNSSAQAF LGPENPEEPY LDGINYNCVA PGK RFRPMD NLSGGEKTVA ALALLFAIHS YKPAPFFVLD EIDAALDNTN IGKVANYIKE QSTCNFQAIV ISLKEEFYTK AESL IGVYP EQGDCVISKV LTFDLTKYPD ANPNPNEQ

UniProtKB: Structural maintenance of chromosomes protein 1A

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Macromolecule #2: Structural maintenance of chromosomes protein 3

MacromoleculeName: Structural maintenance of chromosomes protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 141.771562 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MYIKQVIIQG FRSYRDQTIV DPFSSKHNVI VGRNGSGKSN FFYAIQFVLS DEFSHLRPEQ RLALLHEGTG PRVISAFVEI IFDNSDNRL PIDKEEVSLR RVIGAKKDQY FLDKKMVTKN DVMNLLESAG FSRSNPYYIV KQGKINQMAT APDSQRLKLL R EVAGTRVY ...String:
MYIKQVIIQG FRSYRDQTIV DPFSSKHNVI VGRNGSGKSN FFYAIQFVLS DEFSHLRPEQ RLALLHEGTG PRVISAFVEI IFDNSDNRL PIDKEEVSLR RVIGAKKDQY FLDKKMVTKN DVMNLLESAG FSRSNPYYIV KQGKINQMAT APDSQRLKLL R EVAGTRVY DERKEESISL MKETEGKREK INELLKYIEE RLHTLEEEKE ELAQYQKWDK MRRALEYTIY NQELNETRAK LD ELSAKRE TSGEKSRQLR DAQQDARDKM EDIERQVREL KTKISAMKEE KEQLSAERQE QIKQRTKLEL KAKDLQDELA GNS EQRKRL LKERQKLLEK IEEKQKELAE TEPKFNSVKE KEERGIARLA QATQERTDLY AKQGRGSQFT SKEERDKWIK KELK SLDQA INDKKRQIAA IHKDLEDTEA NKEKNLEQYN KLDQDLNEVK ARVEELDRKY YEVKNKKDEL QSERNYLWRE ENAEQ QALA AKREDLEKKQ QLLRAATGKA ILNGIDSINK VLDHFRRKGI NQHVQNGYHG IVMNNFECEP AFYTCVEVTA GNRLFY HIV DSDEVSTKIL MEFNKMNLPG EVTFLPLNKL DVRDTAYPET NDAIPMISKL RYNPRFDKAF KHVFGKTLIC RSMEVST QL ARAFTMDCIT LEGDQVSHRG ALTGGYYDTR KSRLELQKDV RKAEEELGEL EAKLNENLRR NIERINNEID QLMNQMQQ I ETQQRKFKAS RDSILSEMKM LKEKRQQSEK TFMPKQRSLQ SLEASLHAME STRESLKAEL GTDLLSQLSL EDQKRVDAL NDEIRQLQQE NRQLLNERIK LEGIITRVET YLNENLRKRL DQVEQELNEL RETEGGTVLT ATTSELEAIN KRVKDTMARS EDLDNSIDK TEAGIKELQK SMERWKNMEK EHMDAINHDT KELEKMTNRQ GMLLKKKEEC MKKIRELGSL PQEAFEKYQT L SLKQLFRK LEQCNTELKK YSHVNKKALD QFVNFSEQKE KLIKRQEELD RGYKSIMELM NVLELRKYEA IQLTFKQVSK NF SEVFQKL VPGGKATLVM KKGDVEGSQS QDEGEGSGES ERGSGSQSSV PSVDQFTGVG IRVSFTGKQG EMREMQQLSG GQK SLVALA LIFAIQKCDP APFYLFDEID QALDAQHRKA VSDMIMELAV HAQFITTTFR PELLESADKF YGVKFRNKVS HIDV ITAEM AKDFVEDDTT HG

UniProtKB: Structural maintenance of chromosomes protein 3

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Macromolecule #3: Double-strand-break repair protein rad21 homolog

MacromoleculeName: Double-strand-break repair protein rad21 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.556102 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MFYAHFVLSK RGPLAKIWLA AHWDKKLTKA HVFECNLESS VESIISPKVK MALRTSGHLL LGVVRIYHRK AKYLLADCNE AFIKIKMAF RPGVVDLPEE NREAAYNAIT LPEEFHDFDQ PLPDLDDIDV AQQFSLNQSR VEEITMREEV GNISILQEND F GDFGMDDR ...String:
MFYAHFVLSK RGPLAKIWLA AHWDKKLTKA HVFECNLESS VESIISPKVK MALRTSGHLL LGVVRIYHRK AKYLLADCNE AFIKIKMAF RPGVVDLPEE NREAAYNAIT LPEEFHDFDQ PLPDLDDIDV AQQFSLNQSR VEEITMREEV GNISILQEND F GDFGMDDR EIMAEGSAFE DDDMLVSTTT SNLLLESEQS TSNLNEKINH LEYEDQYKDD NFGEGNDGGI LDDKLISNND GG IFDDPPA LSEAGVMLPE QPAHDDMDED DNVSMGGPDS PASVDPVEPM PTMTDQTTLV PNEEEAFALE PIDITVKETK AKR KRKLIV DSVKELDSKT IRAQLSDYSD IVTTLDLAPP TKKLMMWKET GGVEKLFSLP AQPLWNNRLL KLFTRCLTPL VPED LRKRR KGGEADNLDE FLKEFENPEV PREDQQQQHQ QRDVIDEPII EEPSALQESV MEASRTNIDE SAMPPPPPQG VKRKA GQID PEPVMPPQQV EQMEIPPVEL PPEEPPNICQ LIPELELLPE KEKEKEKEKE DDEEEEDEDA SGGDQDQEER RWNKRT QQM LHGLQRALAK TGAESISLLE LCRNTNRKQA AAKFYSFLVL KKQQAIELTQ EEPYSDIIAT PGPRFHII

UniProtKB: Double-strand-break repair protein rad21 homolog

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Macromolecule #4: Cohesin subunit SA-1

MacromoleculeName: Cohesin subunit SA-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 144.616969 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MITSELPVLQ DSTNETTAHS DAGSELEETE VKGKRKRGRP GRPPSTNKKP RKSPGEKSRI EAGIRGAGRG RANGHPQQNG EGEPVTLFE VVKLGKSAMQ SVVDDWIESY KQDRDIALLD LINFFIQCSG CRGTVRIEMF RNMQNAEIIR KMTEEFDEDS G DYPLTMPG ...String:
MITSELPVLQ DSTNETTAHS DAGSELEETE VKGKRKRGRP GRPPSTNKKP RKSPGEKSRI EAGIRGAGRG RANGHPQQNG EGEPVTLFE VVKLGKSAMQ SVVDDWIESY KQDRDIALLD LINFFIQCSG CRGTVRIEMF RNMQNAEIIR KMTEEFDEDS G DYPLTMPG PQWKKFRSNF CEFIGVLIRQ CQYSIIYDEY MMDTVISLLT GLSDSQVRAF RHTSTLAAMK LMTALVNVAL NL SIHQDNT QRQYEAERNK MIGKRANERL ELLLQKRKEL QENQDEIENM MNSIFKGIFV HRYRDAIAEI RAICIEEIGV WMK MYSDAF LNDSYLKYVG WTLHDRQGEV RLKCLKALQS LYTNRELFPK LELFTNRFKD RIVSMTLDKE YDVAVEAIRL VTLI LHGSE EALSNEDCEN VYHLVYSAHR PVAVAAGEFL HKKLFSRHDP QAEEALAKRR GRNSPNGNLI RMLVLFFLES ELHEH AAYL VDSLWESSQE LLKDWECMTE LLLEEPVQGE EAMSDRQESA LIELMVCTIR QAAEAHPPVG RGTGKRVLTA KERKTQ IDD RNKLTEHFII TLPMLLSKYS ADAEKVANLL QIPQYFDLEI YSTGRMEKHL DALLKQIKFV VEKHVESDVL EACSKTY SI LCSEEYTIQN RVDIARSQLI DEFVDRFNHS VEDLLQEGEE ADDDDIYNVL STLKRLTSFH NAHDLTKWDL FGNCYRLL K TGIEHGAMPE QIVVQALQCS HYSILWQLVK ITDGSPSKED LLVLRKTVKS FLAVCQQCLS NVNTPVKEQA FMLLCDLLM IFSHQLMTGG REGLQPLVFN PDTGLQSELL SFVMDHVFID QDEENQSMEG DEEDEANKIE ALHKRRNLLA AFSKLIIYDI VDMHAAADI FKHYMKYYND YGDIIKETLS KTRQIDKIQC AKTLILSLQQ LFNELVQEQG PNLDRTSAHV SGIKELARRF A LTFGLDQI KTREAVATLH KDGIEFAFKY QNQKGQEYPP PNLAFLEVLS EFSSKLLRQD KKTVHSYLEK FLTEQMMERR ED VWLPLIS YRNSLVTGGE DDRMSVNSGS SSSKTSSVRN KKGRPPLHKK RVEDESLDNT WLNRTDTMIQ TPGPLPAPQL TST VLRENS RPMGDQIQEP ESEHGSEPDF LHNPQMQISW LGQPKLEDLN RKDRTGMNYM KVRTGVRHAV RGLMEEDAEP IFED VMMSS RSQLEDMNEE FEDTMVIDLP PSRNRRERAE LRPDFFDSAA IIEDDSGFGM PMF

UniProtKB: Cohesin subunit SA-1

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Macromolecule #5: Nipped-B-like protein

MacromoleculeName: Nipped-B-like protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 167.830547 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SLSEVARKMK KKEKQKKRKA YEPKLTPEEM MDSSTFKRFT ASIENILDNL EDMDFTAFGD DDEIPQELLL GKHQLNELGS ESAKIKAMG IMDKLSTDKT VKVLNILEKN IQDGSKLSTL LNHNNDTEEE ERLWRDLIME RVTKSADACL TTINIMTSPN M PKAVYIED ...String:
SLSEVARKMK KKEKQKKRKA YEPKLTPEEM MDSSTFKRFT ASIENILDNL EDMDFTAFGD DDEIPQELLL GKHQLNELGS ESAKIKAMG IMDKLSTDKT VKVLNILEKN IQDGSKLSTL LNHNNDTEEE ERLWRDLIME RVTKSADACL TTINIMTSPN M PKAVYIED VIERVIQYTK FHLQNTLYPQ YDPVYRLDPH GGGLLSSKAK RAKCSTHKQR VIVMLYNKVC DIVSSLSELL EI QLLTDTT ILQVSSMGIT PFFVENVSEL QLCAIKLVTA VFSRYEKHRQ LILEEIFTSL ARLPTSKRSL RNFRLNSSDM DGE PMYIQM VTALVLQLIQ CVVHLPSSEK DSNAEEDSNK KIDQDVVITN SYETAMRTAQ NFLSIFLKKC GSKQGEEDYR PLFE NFVQD LLSTVNKPEW PAAELLLSLL GRLLVHQFSN KSTEMALRVA SLDYLGTVAA RLRKDAVTSK MDQGSIERIL KQVSG GEDE IQQLQKALLD YLDENTETDP SLVFSRKFYI AQWFRDTTLE TEKAMKSQKD EESSEGTHHA KEIETTGQIM HRAENR KKF LRSIIKTTPS QFSTLKMNSD TVDYDDACLI VRYLASMRPF AQSFDIYLTQ ILRVLGENAI AVRTKAMKCL SEVVAVD PS ILARLDMQRG VHGRLMDNST SVREAAVELL GRFVLCRPQL AEQYYDMLIE RILDTGISVR KRVIKILRDI CIEQPTFP K ITEMCVKMIR RVNDEEGIKK LVNETFQKLW FTPTPHNDKE AMTRKILNIT DVVAACRDTG YDWFEQLLQN LLKSEEDSS YKPVKKACTQ LVDNLVEHIL KYEESLADSD NKGVNSGRLV ACITTLFLFS KIRPQLMVKH AMTMQPYLTT KCSTQNDFMV ICNVAKILE LVVPLMEHPS ETFLATIEED LMKLIIKYGM TVVQHCVSCL GAVVNKVTQN FKFVWACFNR YYGAISKLKS Q HQEDPNNT SLLTNKPALL RSLFTVGALC RHFDFDLEDF KGNSKVNIKD KVLELLMYFT KHSDEEVQTK AIIGLGFAFI QH PSLMFEQ EVKNLYNNIL SDKNSSVNLK IQVLKNLQTY LQEEDTRMQQ ADRDWKKVAK QEDLKEMGDV SSGMSSSIMQ LYL KQVLEA FFHTQSSVRH FALNVIALTL NQGLIHPVQC VPYLIAMGTD PEPAMRNKAD QQLVEIDKKY AGFIHMKAVA GMKM SYQVQ QAINTCLKDP VRGFRQDESS SALCSHLYSM IRGNRQHRRA FLISLLNLFD DTAKTDVTML LYIADNLACF PYQTQ EEPL FIMHHIDITL SVSGSNLLQS FKESMVKDKR KERKSSPSKE NESSDSEEEV SRPRKSRKRV DSDSDSDSED DINSVM KCL PENSAPLIEF ANVSQGILLL LMLKQHLKNL CGFSDSKIQK YSPSESAKVY DKAINRKTGV HFHPKQTLDF LRSDMAN SK ITEEVKRSIV KQYLDFKLLM EHLDP

UniProtKB: Nipped-B-like protein

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Macromolecule #8: Transcriptional repressor CTCF

MacromoleculeName: Transcriptional repressor CTCF / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.928758 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEGDAVEAIV EESETFIKGK ERKTYQRRRE GGQEEDACHL PQNQTDGGEV VQDVNSSVQM VMMEQLDPTL LQMKTEVMEG TVAPEAEAA VDDTQIITLQ VVNMEEQPIN IGELQLVQVP VPVTVPVATT SVEELQGAYE NEVSKEGLAE SEPMICHTLP L PEGFQVVK ...String:
MEGDAVEAIV EESETFIKGK ERKTYQRRRE GGQEEDACHL PQNQTDGGEV VQDVNSSVQM VMMEQLDPTL LQMKTEVMEG TVAPEAEAA VDDTQIITLQ VVNMEEQPIN IGELQLVQVP VPVTVPVATT SVEELQGAYE NEVSKEGLAE SEPMICHTLP L PEGFQVVK VGANGEVETL EQGELPPQED PSWQKDPDYQ PPAKKTKKTK KSKLRYTEEG KDVDVSVYDF EEEQQEGLLS EV NAEKVVG NMKPPKPTKI KKKGVKKTFQ CELCSYTCPR RSNLDRHMKS HTDERPHKCH LCGRAFRTVT LLRNHLNTHT GTR PHKCPD CDMAFVTSGE LVRHRRYKHT HEKPFKCSMC DYASVEVSKL KRHIRSHTGE RPFQCSLCSY ASRDTYKLKR HMRT HSGEK PYECYICHAR FTQSGTMKMH ILQKHTENVA KFHCPHCDTV IARKSDLGVH LRKQHSYIEQ GKKCRYCDAV FHERY ALIQ HQKSHKNEKR FKCDQCDYAC RQERHMIMHK RTHTGEKPYA CSHCDKTFRQ KQLLDMHFKR YHDPNFVPAA FVCSKC GKT FTRRNTMARH ADNCAGPDGV EGENGGETKK SKRGRKRKMR SKKEDSSDSE NAEPDLDDNE DEEEPAVEIE PEPEPQP VT PAPPPAKKRR GRPPGRTNQP KQNQPTAIIQ VEDQNTGAIE NIIVEVKKEP DAEPAEGEEE EAQPAATDAP NGDLTPEM I LSMMDR

UniProtKB: Transcriptional repressor CTCF

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Macromolecule #6: DNA (118-MER)

MacromoleculeName: DNA (118-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.202281 KDa
SequenceString: (DG)(DA)(DT)(DA)(DA)(DA)(DT)(DT)(DC)(DT) (DT)(DG)(DT)(DT)(DT)(DT)(DC)(DA)(DT)(DA) (DT)(DC)(DC)(DT)(DA)(DA)(DA)(DA)(DT) (DT)(DA)(DA)(DA)(DG)(DG)(DG)(DA)(DA)(DA) (DA) (DT)(DA)(DA)(DA)(DC)(DA) ...String:
(DG)(DA)(DT)(DA)(DA)(DA)(DT)(DT)(DC)(DT) (DT)(DG)(DT)(DT)(DT)(DT)(DC)(DA)(DT)(DA) (DT)(DC)(DC)(DT)(DA)(DA)(DA)(DA)(DT) (DT)(DA)(DA)(DA)(DG)(DG)(DG)(DA)(DA)(DA) (DA) (DT)(DA)(DA)(DA)(DC)(DA)(DA)(DT) (DA)(DC)(DA)(DT)(DA)(DA)(DC)(DA)(DA)(DA) (DA)(DC) (DA)(DT)(DA)(DT)(DA)(DA)(DA) (DA)(DA)(DC)(DC)(DA)(DC)(DC)(DT)(DC)(DA) (DC)(DT)(DA) (DG)(DC)(DG)(DC)(DC)(DC) (DC)(DC)(DT)(DG)(DC)(DT)(DG)(DG)(DC)(DC) (DT)(DC)(DT)(DG) (DT)(DG)(DG)(DG)(DC) (DA)(DC)(DT)(DG)(DC)(DA)(DA)(DT)(DC)(DT) (DT)(DG)(DC)

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Macromolecule #7: DNA (118-MER)

MacromoleculeName: DNA (118-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.605387 KDa
SequenceString: (DG)(DC)(DA)(DA)(DG)(DA)(DT)(DT)(DG)(DC) (DA)(DG)(DT)(DG)(DC)(DC)(DC)(DA)(DC)(DA) (DG)(DA)(DG)(DG)(DC)(DC)(DA)(DG)(DC) (DA)(DG)(DG)(DG)(DG)(DG)(DC)(DG)(DC)(DT) (DA) (DG)(DT)(DG)(DA)(DG)(DG) ...String:
(DG)(DC)(DA)(DA)(DG)(DA)(DT)(DT)(DG)(DC) (DA)(DG)(DT)(DG)(DC)(DC)(DC)(DA)(DC)(DA) (DG)(DA)(DG)(DG)(DC)(DC)(DA)(DG)(DC) (DA)(DG)(DG)(DG)(DG)(DG)(DC)(DG)(DC)(DT) (DA) (DG)(DT)(DG)(DA)(DG)(DG)(DT)(DG) (DG)(DT)(DT)(DT)(DT)(DT)(DA)(DT)(DA)(DT) (DG)(DT) (DT)(DT)(DT)(DG)(DT)(DT)(DA) (DT)(DG)(DT)(DA)(DT)(DT)(DG)(DT)(DT)(DT) (DA)(DT)(DT) (DT)(DT)(DC)(DC)(DC)(DT) (DT)(DT)(DA)(DA)(DT)(DT)(DT)(DT)(DA)(DG) (DG)(DA)(DT)(DA) (DT)(DG)(DA)(DA)(DA) (DA)(DC)(DA)(DA)(DG)(DA)(DA)(DT)(DT)(DT) (DA)(DT)(DC)

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #10: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 11 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2185704
Startup modelType of model: EMDB MAP
EMDB ID:

21658

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 42704
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationNumber classes: 5 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6wge

source_name: PDB, initial_model_type: experimental model

5t0u

source_name: PDB, initial_model_type: experimental model

5yef

source_name: PDB, initial_model_type: experimental model

5yel

source_name: PDB, initial_model_type: experimental model

6qnx

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7w1m:
Cryo-EM structure of human cohesin-CTCF-DNA complex

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