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- EMDB-21663: Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1 -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21663 | |||||||||
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Title | Cryo-EM structure of human Cohesin-NIPBL-DNA complex without STAG1 | |||||||||
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![]() | Protein-DNA complex / ATPase / DNA-binding protein / Genome organization / Sister chromatid cohesion / Transcription regulation / CELL CYCLE / CELL CYCLE-DNA complex | |||||||||
Function / homology | ![]() eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / cohesin loader activity / response to DNA damage checkpoint signaling / regulation of hair cycle ...eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / cohesin loader activity / response to DNA damage checkpoint signaling / regulation of hair cycle / negative regulation of mitotic metaphase/anaphase transition / 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 / embryonic viscerocranium morphogenesis / establishment of meiotic sister chromatid cohesion / cohesin complex / mitotic cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / uterus morphogenesis / negative regulation of glial cell apoptotic process / establishment of protein localization to chromatin / regulation of developmental growth / embryonic digestive tract morphogenesis / replication-born double-strand break repair via sister chromatid exchange / cellular response to X-ray / lateral element / positive regulation of neuron migration / integrator complex / mediator complex binding / chromo shadow domain binding / establishment of mitotic sister chromatid cohesion / positive regulation of multicellular organism growth / metanephros development / chromatin looping / positive regulation of ossification / digestive tract development / reciprocal meiotic recombination / embryonic forelimb morphogenesis / sister chromatid cohesion / face morphogenesis / lncRNA binding / negative regulation of interleukin-1 beta production / microtubule motor activity / mitotic sister chromatid cohesion / stem cell population maintenance / dynein complex binding / mitotic spindle pole / fat cell differentiation / beta-tubulin binding / outflow tract morphogenesis / regulation of DNA replication / mitotic sister chromatid segregation / somatic stem cell population maintenance / positive regulation of interleukin-10 production / regulation of embryonic development / 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 / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / promoter-specific chromatin binding / sensory perception of sound / response to radiation / brain development / kinetochore / cognition / spindle pole / histone deacetylase binding / nuclear matrix / Separation of Sister Chromatids / transcription corepressor activity / double-strand break repair / protein localization / 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 / chromatin remodeling / protein heterodimerization activity / cell division / intracellular membrane-bounded organelle / DNA repair / DNA damage response / chromatin binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Shi ZB / Gao H / Bai XC / Yu H | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21 KB 21 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 136.4 KB | ||
Filedesc metadata | ![]() | 9.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wgeMC ![]() 6wg3C ![]() 6wg4C ![]() 6wg6C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Human Cohesin-NIPBL-DNA Complex without STAG1
Entire | Name: Human Cohesin-NIPBL-DNA Complex without STAG1 |
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Components |
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-Supramolecule #1: Human Cohesin-NIPBL-DNA Complex without STAG1
Supramolecule | Name: Human Cohesin-NIPBL-DNA Complex without STAG1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 820 KDa |
-Macromolecule #1: Structural maintenance of chromosomes protein 1A
Macromolecule | Name: Structural maintenance of chromosomes protein 1A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 143.484109 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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
Macromolecule | Name: Structural maintenance of chromosomes protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 141.770578 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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
Macromolecule | Name: Double-strand-break repair protein rad21 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 71.556102 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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: Nipped-B-like protein
Macromolecule | Name: Nipped-B-like protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 186.77825 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: PSLSEVARKM KKKEKQKKRK AYEPKLTPEE MMDSSTFKRF TASIENILDN LEDMDFTAFG DDDEIPQELL LGKHQLNELG SESAKIKAM GIMDKLSTDK TVKVLNILEK NIQDGSKLST LLNHNNDTEE EERLWRDLIM ERVTKSADAC LTTINIMTSP N MPKAVYIE ...String: PSLSEVARKM KKKEKQKKRK AYEPKLTPEE MMDSSTFKRF TASIENILDN LEDMDFTAFG DDDEIPQELL LGKHQLNELG SESAKIKAM GIMDKLSTDK TVKVLNILEK NIQDGSKLST LLNHNNDTEE EERLWRDLIM ERVTKSADAC LTTINIMTSP N MPKAVYIE DVIERVIQYT KFHLQNTLYP QYDPVYRLDP HGGGLLSSKA KRAKCSTHKQ RVIVMLYNKV CDIVSSLSEL LE IQLLTDT TILQVSSMGI TPFFVENVSE LQLCAIKLVT AVFSRYEKHR QLILEEIFTS LARLPTSKRS LRNFRLNSSD MDG EPMYIQ MVTALVLQLI QCVVHLPSSE KDSNAEEDSN KKIDQDVVIT NSYETAMRTA QNFLSIFLKK CGSKQGEEDY RPLF ENFVQ DLLSTVNKPE WPAAELLLSL LGRLLVHQFS NKSTEMALRV ASLDYLGTVA ARLRKDAVTS KMDQGSIERI LKQVS GGED EIQQLQKALL DYLDENTETD PSLVFSRKFY IAQWFRDTTL ETEKAMKSQK DEESSEGTHH AKEIETTGQI MHRAEN RKK FLRSIIKTTP SQFSTLKMNS DTVDYDDACL IVRYLASMRP FAQSFDIYLT QILRVLGENA IAVRTKAMKC LSEVVAV DP SILARLDMQR GVHGRLMDNS TSVREAAVEL LGRFVLCRPQ LAEQYYDMLI ERILDTGISV RKRVIKILRD ICIEQPTF P KITEMCVKMI RRVNDEEGIK KLVNETFQKL WFTPTPHNDK EAMTRKILNI TDVVAACRDT GYDWFEQLLQ NLLKSEEDS SYKPVKKACT QLVDNLVEHI LKYEESLADS DNKGVNSGRL VACITTLFLF SKIRPQLMVK HAMTMQPYLT TKCSTQNDFM VICNVAKIL ELVVPLMEHP SETFLATIEE DLMKLIIKYG MTVVQHCVSC LGAVVNKVTQ NFKFVWACFN RYYGAISKLK S QHQEDPNN TSLLTNKPAL LRSLFTVGAL CRHFDFDLED FKGNSKVNIK DKVLELLMYF TKHSDEEVQT KAIIGLGFAF IQ HPSLMFE QEVKNLYNNI LSDKNSSVNL KIQVLKNLQT YLQEEDTRMQ QADRDWKKVA KQEDLKEMGD VSSGMSSSIM QLY LKQVLE AFFHTQSSVR HFALNVIALT LNQGLIHPVQ CVPYLIAMGT DPEPAMRNKA DQQLVEIDKK YAGFIHMKAV AGMK MSYQV QQAINTCLKD PVRGFRQDES SSALCSHLYS MIRGNRQHRR AFLISLLNLF DDTAKTDVTM LLYIADNLAC FPYQT QEEP LFIMHHIDIT LSVSGSNLLQ SFKESMVKDK RKERKSSPSK ENESSDSEEE VSRPRKSRKR VDSDSDSDSE DDINSV MKC LPENSAPLIE FANVSQGILL LLMLKQHLKN LCGFSDSKIQ KYSPSESAKV YDKAINRKTG VHFHPKQTLD FLRSDMA NS KITEEVKRSI VKQYLDFKLL MEHLDPDEEE EEGEVSASTN ARNKAITSLL GGGSPKNNTA AETEDDESDG EDRGGGTS G SLRRSKRNSD STELAAQMNE SVDVMDVIAI CCPKYKDRPQ IARVVQKTSS GFSVQWMAGS YSGSWTEAKR RDGRKLVPW VDTIKESDII YKKIALTSAN KLTNKVVQTL RSLYAAKDGT SS UniProtKB: Nipped-B-like protein |
-Macromolecule #5: DNA (43-MER)
Macromolecule | Name: DNA (43-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.422931 KDa |
Sequence | String: (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 #6: DNA (43-MER)
Macromolecule | Name: DNA (43-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.035333 KDa |
Sequence | String: (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 #7: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 7 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ![]() ChemComp-ANP: |
-Macromolecule #8: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 5796 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | ![]() PDB-6wge: |