[English] 日本語
Yorodumi
- EMDB-21658: Cryo-EM structure of human Cohesin-NIPBL-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21658
TitleCryo-EM structure of human Cohesin-NIPBL-DNA complex
Map dataHuman Cohesin-NIPBL-DNA complex
Sample
  • Complex: Human Cohesin-NIPBL-DNA Complex
    • 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
    • DNA: DNA (51-MER)
    • DNA: DNA (51-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsProtein-DNA complex / ATPase / DNA-binding protein / Genome organization / Sister chromatid cohesion / Transcription regulation / CELL CYCLE / CELL CYCLE-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 / mitotic cohesin loading / response to DNA damage checkpoint signaling / regulation of hair cycle / negative regulation of mitotic metaphase/anaphase transition ...eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / response to DNA damage checkpoint signaling / regulation of hair cycle / negative regulation of mitotic metaphase/anaphase transition / cohesin loader activity / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / maintenance of mitotic sister chromatid cohesion / Establishment of Sister Chromatid Cohesion / forelimb morphogenesis / integrator complex / embryonic viscerocranium morphogenesis / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / uterus morphogenesis / establishment of protein localization to chromatin / negative regulation of glial cell apoptotic process / regulation of developmental growth / embryonic digestive tract morphogenesis / replication-born double-strand break repair via sister chromatid exchange / positive regulation of neuron migration / cellular response to X-ray / lateral element / chromo shadow domain binding / mediator complex binding / establishment of mitotic sister chromatid cohesion / chromatin looping / positive regulation of multicellular organism growth / metanephros development / digestive tract development / positive regulation of ossification / reciprocal meiotic recombination / lncRNA binding / embryonic forelimb morphogenesis / sister chromatid cohesion / face morphogenesis / negative regulation of interleukin-1 beta production / mitotic sister chromatid cohesion / microtubule motor activity / dynein complex binding / stem cell population maintenance / beta-tubulin binding / fat cell differentiation / mitotic spindle pole / outflow tract morphogenesis / mitotic sister chromatid segregation / somatic stem cell population maintenance / regulation of DNA replication / regulation of embryonic development / positive regulation of interleukin-10 production / chromosome, centromeric region / negative regulation of tumor necrosis factor production / mitotic spindle assembly / developmental growth / localization / SUMOylation of DNA damage response and repair proteins / heart morphogenesis / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / meiotic cell cycle / condensed nuclear chromosome / chromosome segregation / promoter-specific chromatin binding / sensory perception of sound / brain development / response to radiation / protein localization / kinetochore / cognition / nuclear matrix / spindle pole / histone deacetylase binding / Separation of Sister Chromatids / transcription corepressor activity / double-strand break repair / mitotic cell cycle / chromosome / midbody / double-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / nuclear body / chromatin remodeling / protein heterodimerization activity / cell division / DNA repair / intracellular membrane-bounded organelle
Similarity search - Function
: / Sister chromatid cohesion C-terminal domain / HEAT repeat associated with sister chromatid cohesion protein / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein ...: / Sister chromatid cohesion C-terminal domain / HEAT repeat associated with sister chromatid cohesion protein / Scc2/Nipped-B family / Sister chromatid cohesion C-terminus / HEAT repeat associated with sister chromatid cohesion / Smc1, ATP-binding cassette domain / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Structural maintenance of chromosomes 3, ABC domain, eukaryotic / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / Stromalin conservative domain / STAG / Stromalin conservative domain / Cohesin subunit Scc3/SA / STAG domain / Stromalin conservative (SCD) domain profile. / 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 / 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 / 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: 5.3 Å
AuthorsShi ZB / Gao H / Yu H / Bai X
Funding support United States, 2 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT) United States
Welch Foundation United States
CitationJournal: Science / Year: 2020
Title: Cryo-EM structure of the human cohesin-NIPBL-DNA complex.
Authors: Zhubing Shi / Haishan Gao / Xiao-Chen Bai / Hongtao Yu /
Abstract: As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How ...As a ring-shaped adenosine triphosphatase (ATPase) machine, cohesin organizes the eukaryotic genome by extruding DNA loops and mediates sister chromatid cohesion by topologically entrapping DNA. How cohesin executes these fundamental DNA transactions is not understood. Using cryo-electron microscopy (cryo-EM), we determined the structure of human cohesin bound to its loader NIPBL and DNA at medium resolution. Cohesin and NIPBL interact extensively and together form a central tunnel to entrap a 72-base pair DNA. NIPBL and DNA promote the engagement of cohesin's ATPase head domains and ATP binding. The hinge domains of cohesin adopt an "open washer" conformation and dock onto the STAG1 subunit. Our structure explains the synergistic activation of cohesin by NIPBL and DNA and provides insight into DNA entrapment by cohesin.
History
DepositionApr 4, 2020-
Header (metadata) releaseMay 20, 2020-
Map releaseMay 20, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wg3
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21658.png

Downloads & links

-
Map

FileDownload / File: emd_21658.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Cohesin-NIPBL-DNA complex
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.022066671 - 0.07254982
Average (Standard dev.)0.00075202546 (±0.004226073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 321.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z321.600321.600321.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0220.0730.001

-
Supplemental data

-
Sample components

-
Entire : Human Cohesin-NIPBL-DNA Complex

EntireName: Human Cohesin-NIPBL-DNA Complex
Components
  • Complex: Human Cohesin-NIPBL-DNA Complex
    • 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
    • DNA: DNA (51-MER)
    • DNA: DNA (51-MER)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

-
Supramolecule #1: Human Cohesin-NIPBL-DNA Complex

SupramoleculeName: Human Cohesin-NIPBL-DNA Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 820 KDa

-
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: 143.484109 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 QIDAALDNTN IGKVANYIKE QSTCNFQAIV ISLKEEFYTK AESL IGVYP EQGDCVISKV LTFDLTKYPD ANPNPNEQ

UniProtKB: Structural maintenance of chromosomes protein 1A

-
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: 141.770578 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 APFYLFDQID QALDAQHRKA VSDMIMELAV HAQFITTTFR PELLESADKF YGVKFRNKVS HIDV ITAEM AKDFVEDDTT HG

UniProtKB: Structural maintenance of chromosomes protein 3

-
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

-
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: 146.075656 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 PMFGAPMRSG ALEVLFQ

UniProtKB: Cohesin subunit SA-1

-
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: 188.151688 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSYYHHHHHH PSLSEVARKM KKKEKQKKRK AYEPKLTPEE MMDSSTFKRF TASIENILDN LEDMDFTAFG DDDEIPQELL LGKHQLNEL GSESAKIKAM GIMDKLSTDK TVKVLNILEK NIQDGSKLST LLNHNNDTEE EERLWRDLIM ERVTKSADAC L TTINIMTS ...String:
MSYYHHHHHH PSLSEVARKM KKKEKQKKRK AYEPKLTPEE MMDSSTFKRF TASIENILDN LEDMDFTAFG DDDEIPQELL LGKHQLNEL GSESAKIKAM GIMDKLSTDK TVKVLNILEK NIQDGSKLST LLNHNNDTEE EERLWRDLIM ERVTKSADAC L TTINIMTS PNMPKAVYIE DVIERVIQYT KFHLQNTLYP QYDPVYRLDP HGGGLLSSKA KRAKCSTHKQ RVIVMLYNKV CD IVSSLSE LLEIQLLTDT TILQVSSMGI TPFFVENVSE LQLCAIKLVT AVFSRYEKHR QLILEEIFTS LARLPTSKRS LRN FRLNSS DMDGEPMYIQ MVTALVLQLI QCVVHLPSSE KDSNAEEDSN KKIDQDVVIT NSYETAMRTA QNFLSIFLKK CGSK QGEED YRPLFENFVQ DLLSTVNKPE WPAAELLLSL LGRLLVHQFS NKSTEMALRV ASLDYLGTVA ARLRKDAVTS KMDQG SIER ILKQVSGGED EIQQLQKALL DYLDENTETD PSLVFSRKFY IAQWFRDTTL ETEKAMKSQK DEESSEGTHH AKEIET TGQ IMHRAENRKK FLRSIIKTTP SQFSTLKMNS DTVDYDDACL IVRYLASMRP FAQSFDIYLT QILRVLGENA IAVRTKA MK CLSEVVAVDP SILARLDMQR GVHGRLMDNS TSVREAAVEL LGRFVLCRPQ LAEQYYDMLI ERILDTGISV RKRVIKIL R DICIEQPTFP KITEMCVKMI RRVNDEEGIK KLVNETFQKL WFTPTPHNDK EAMTRKILNI TDVVAACRDT GYDWFEQLL QNLLKSEEDS SYKPVKKACT QLVDNLVEHI LKYEESLADS DNKGVNSGRL VACITTLFLF SKIRPQLMVK HAMTMQPYLT TKCSTQNDF MVICNVAKIL ELVVPLMEHP SETFLATIEE DLMKLIIKYG MTVVQHCVSC LGAVVNKVTQ NFKFVWACFN R YYGAISKL KSQHQEDPNN TSLLTNKPAL LRSLFTVGAL CRHFDFDLED FKGNSKVNIK DKVLELLMYF TKHSDEEVQT KA IIGLGFA FIQHPSLMFE QEVKNLYNNI LSDKNSSVNL KIQVLKNLQT YLQEEDTRMQ QADRDWKKVA KQEDLKEMGD VSS GMSSSI MQLYLKQVLE AFFHTQSSVR HFALNVIALT LNQGLIHPVQ CVPYLIAMGT DPEPAMRNKA DQQLVEIDKK YAGF IHMKA VAGMKMSYQV QQAINTCLKD PVRGFRQDES SSALCSHLYS MIRGNRQHRR AFLISLLNLF DDTAKTDVTM LLYIA DNLA CFPYQTQEEP LFIMHHIDIT LSVSGSNLLQ SFKESMVKDK RKERKSSPSK ENESSDSEEE VSRPRKSRKR VDSDSD SDS EDDINSVMKC LPENSAPLIE FANVSQGILL LLMLKQHLKN LCGFSDSKIQ KYSPSESAKV YDKAINRKTG VHFHPKQ TL DFLRSDMANS KITEEVKRSI VKQYLDFKLL MEHLDPDEEE EEGEVSASTN ARNKAITSLL GGGSPKNNTA AETEDDES D GEDRGGGTSG SLRRSKRNSD STELAAQMNE SVDVMDVIAI CCPKYKDRPQ IARVVQKTSS GFSVQWMAGS YSGSWTEAK RRDGRKLVPW VDTIKESDII YKKIALTSAN KLTNKVVQTL RSLYAAKDGT SS

UniProtKB: Nipped-B-like protein

-
Macromolecule #6: DNA (51-MER)

MacromoleculeName: DNA (51-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.928584 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)

-
Macromolecule #7: DNA (51-MER)

MacromoleculeName: DNA (51-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.468875 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)

-
Macromolecule #8: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 8 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5796 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 510507
Startup modelType of model: NONE
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 6857
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6wg3:
Cryo-EM structure of human Cohesin-NIPBL-DNA complex

+
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