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- EMDB-51190: High-resolution structure of the Anaphase-promoting complex/cyclo... -

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Basic information

Entry
Database: EMDB / ID: EMD-51190
TitleHigh-resolution structure of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-activator Cdh1
Map dataComposite map (unsharpened) of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1
Sample
  • Complex: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
    • Protein or peptide: x 14 types
  • Protein or peptide: x 2 types
  • Ligand: x 1 types
KeywordsAPC/C / cyclosome / Cdc20 / Cdh1 / ubiquitination / Emi1 / mitosis / Cell cycle
Function / homology
Function and homology information


negative regulation of DNA endoreduplication / positive regulation of biomineral tissue development / negative regulation of meiotic nuclear division / negative regulation of mitotic metaphase/anaphase transition / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mesenchymal stem cell migration / Mitotic Metaphase/Anaphase Transition / regulation of meiotic nuclear division / negative regulation of ubiquitin-protein transferase activity / positive regulation of synapse maturation ...negative regulation of DNA endoreduplication / positive regulation of biomineral tissue development / negative regulation of meiotic nuclear division / negative regulation of mitotic metaphase/anaphase transition / positive regulation of anaphase-promoting complex-dependent catabolic process / positive regulation of mesenchymal stem cell migration / Mitotic Metaphase/Anaphase Transition / regulation of meiotic nuclear division / negative regulation of ubiquitin-protein transferase activity / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / vesicle organization / protein branched polyubiquitination / metaphase/anaphase transition of mitotic cell cycle / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / lens fiber cell differentiation / positive regulation of synaptic plasticity / Phosphorylation of the APC/C / regulation of exit from mitosis / anaphase-promoting complex binding / positive regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / spindle assembly involved in female meiosis I / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / protein K11-linked ubiquitination / meiotic spindle / oocyte maturation / regulation of mitotic metaphase/anaphase transition / ubiquitin-ubiquitin ligase activity / regulation of mitotic nuclear division / molecular function inhibitor activity / mitotic metaphase chromosome alignment / negative regulation of ubiquitin protein ligase activity / G1/S-Specific Transcription / mitotic G2 DNA damage checkpoint signaling / microtubule polymerization / Regulation of APC/C activators between G1/S and early anaphase / regulation of DNA replication / cullin family protein binding / Transcriptional Regulation by VENTX / negative regulation of cellular senescence / ubiquitin ligase inhibitor activity / enzyme-substrate adaptor activity / positive regulation of axon extension / ubiquitin-like ligase-substrate adaptor activity / positive regulation of osteoblast differentiation / heterochromatin / protein K48-linked ubiquitination / intercellular bridge / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of G2/M transition of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / regulation of mitotic cell cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / brain development / kinetochore / CDK-mediated phosphorylation and removal of Cdc6 / spindle / neuron projection development / ubiquitin-protein transferase activity / mitotic spindle / Separation of Sister Chromatids / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / mitotic cell cycle / microtubule cytoskeleton / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein phosphatase binding / molecular adaptor activity / nuclear membrane / cell differentiation / protein ubiquitination / cell division / negative regulation of gene expression / DNA repair / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / DNA damage response / protein kinase binding / nucleolus / zinc ion binding
Similarity search - Function
Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / F-box domain / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / : / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / : ...Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / F-box domain / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / : / CDC20/Fizzy WD40 domain / The WD repeat Cdc20/Fizzy family / : / APC4, WD40 domain C-terminal half / Anaphase-promoting complex subunit 4, metazoa / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : / : / : / Anaphase-promoting complex subunit 1 WD40 beta-propeller domain / Anaphase-promoting complex sub unit 1 C-terminal domain / Anaphase-promoting complex subunit 1 middle domain / APC1 beta sandwich domain / Anaphase-promoting complex subunit 5, N-terminal domain / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex, subunit 16 / Cdc23 / Apc13 / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 4 long domain / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 5 domain / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex, cyclosome, subunit 4 / Anaphase-promoting complex subunit APC10/Doc1 / Anaphase-promoting complex, subunit CDC26 / Anaphase-promoting complex APC subunit CDC26 / Anaphase-promoting complex subunit 11, RING-H2 finger / Anaphase-promoting complex subunit 11 RING-H2 finger / Anaphase-promoting complex subunit 2, C-terminal / Anaphase-promoting complex subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase promoting complex (APC) subunit 2 / IBR domain / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Anaphase-promoting complex, cyclosome, subunit 3 / TPR repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / F-box domain / Tetratricopeptide repeat / : / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 11 / Cell division cycle protein 23 homolog / Anaphase-promoting complex subunit 7 ...Cell division cycle protein 27 homolog / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 11 / Cell division cycle protein 23 homolog / Anaphase-promoting complex subunit 7 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 2 / F-box only protein 5 / Fizzy-related protein homolog / Anaphase-promoting complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHoefler A / Yu J / Chang L / Zhang Z / Yang J / Boland A / Barford D
Funding support Switzerland, United Kingdom, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_185235 Switzerland
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Cryo-EM structures of apo-APC/C and APC/C complexes provide insights into APC/C regulation.
Authors: Anna Höfler / Jun Yu / Jing Yang / Ziguo Zhang / Leifu Chang / Stephen H McLaughlin / Geoffrey W Grime / Elspeth F Garman / Andreas Boland / David Barford /
Abstract: APC/C is a multi-subunit complex that functions as a master regulator of cell division. It controls progression through the cell cycle by timely marking mitotic cyclins and other cell cycle ...APC/C is a multi-subunit complex that functions as a master regulator of cell division. It controls progression through the cell cycle by timely marking mitotic cyclins and other cell cycle regulatory proteins for degradation. The APC/C itself is regulated by the sequential action of its coactivator subunits CDC20 and CDH1, post-translational modifications, and its inhibitory binding partners EMI1 and the mitotic checkpoint complex. In this study, we took advantage of developments in cryo-electron microscopy to determine the structures of human APC/C and apo-APC/C at 2.9 Å and 3.2 Å resolution, respectively, providing insights into the regulation of APC/C activity. The high-resolution maps allow the unambiguous assignment of an α-helix to the N-terminus of CDH1 (CDH1) in the APC/C ternary complex. We also identify a zinc-binding module in APC2 that confers structural stability to the complex, and we confirm the presence of zinc ions experimentally. Finally, due to the higher resolution and well defined density of these maps, we are able to build, aided by AlphaFold predictions, several intrinsically disordered regions in different APC/C subunits that likely play a role in proper APC/C assembly and regulation of its activity.
History
DepositionJul 29, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_51190.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map (unsharpened) of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.05 Å/pix.
x 60 pix.
= 423. Å		7.05 Å/pix.
x 60 pix.
= 423. Å		7.05 Å/pix.
x 60 pix.
= 423. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.1.071.071.07
CCP4 map header7.057.057.05
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.6961393 - 2.5556142
Average (Standard dev.)0.02147366 (±0.103095844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Anaphase-promoting complex (APC/C) bound to co-activator Cdh1

EntireName: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
Components
  • Complex: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
    • Protein or peptide: Anaphase-promoting complex subunit 10
    • Protein or peptide: Anaphase-promoting complex subunit 15
    • Protein or peptide: Anaphase-promoting complex subunit 1
    • Protein or peptide: Anaphase-promoting complex subunit 2
    • Protein or peptide: Anaphase-promoting complex subunit 4
    • Protein or peptide: Anaphase-promoting complex subunit 5
    • Protein or peptide: F-box only protein 5
    • Protein or peptide: Cell division cycle protein 16 homolog
    • Protein or peptide: Anaphase-promoting complex subunit CDC26
    • Protein or peptide: Anaphase-promoting complex subunit 13
    • Protein or peptide: Anaphase-promoting complex subunit 16
    • Protein or peptide: Cell division cycle protein 27 homolog
    • Protein or peptide: Anaphase-promoting complex subunit 7
    • Protein or peptide: Cell division cycle protein 23 homolog
  • Protein or peptide: Fizzy-related protein homolog
  • Protein or peptide: Anaphase-promoting complex subunit 11
  • Ligand: ZINC ION

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Supramolecule #1: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1

SupramoleculeName: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: Anaphase-promoting complex subunit 10

MacromoleculeName: Anaphase-promoting complex subunit 10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.282143 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MTTPNKTPPG ADPKQLERTG TVREIGSQAV WSLSSCKPGF GVDQLRDDNL ETYWQSDGSQ PHLVNIQFRR KTTVKTLCIY ADYKSDESY TPSKISVRVG NNFHNLQEIR QLELVEPSGW IHVPLTDNHK KPTRTFMIQI AVLANHQNGR DTHMRQIKIY T PVEESSIG KFPRCTTIDF MMYRSIR

UniProtKB: Anaphase-promoting complex subunit 10

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Macromolecule #2: Anaphase-promoting complex subunit 15

MacromoleculeName: Anaphase-promoting complex subunit 15 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.286727 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSTLFPSLFP RVTETLWFNL DRPCVEETEL QQQEQQHQAW LQSIAEKDNN LVPIGKPASE HYDDEEEEDD EDDEDSEEDS EDDEDMQDM DEMNDYNESP DDGEVNEVDM EGNEQDQDQW MI

UniProtKB: Anaphase-promoting complex subunit 15

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Macromolecule #3: Anaphase-promoting complex subunit 1

MacromoleculeName: Anaphase-promoting complex subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 216.725469 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSNFYEERTT MIAARDLQEF VPFGRDHCKH HPNALNLQLR QLQPASELWS SDGAAGLVGS LQEVTIHEKQ KESWQLRKGV SEIGEDVDY DEELYVAGNM VIWSKGSKSQ ALAVYKAFTV DSPVQQALWC DFIISQDKSE KAYSSNEVEK CICILQSSCI N MHSIEGKD ...String:
MSNFYEERTT MIAARDLQEF VPFGRDHCKH HPNALNLQLR QLQPASELWS SDGAAGLVGS LQEVTIHEKQ KESWQLRKGV SEIGEDVDY DEELYVAGNM VIWSKGSKSQ ALAVYKAFTV DSPVQQALWC DFIISQDKSE KAYSSNEVEK CICILQSSCI N MHSIEGKD YIASLPFQVA NVWPTKYGLL FERSASSHEV PPGSPREPLP TMFSMLHPLD EITPLVCKSG SLFGSSRVQY VV DHAMKIV FLNTDPSIVM TYDAVQNVHS VWTLRRVKSE EENVVLKFSE QGGTPQNVAT SSSLTAHLRS LSKGDSPVTS PFQ NYSSIH SQSRSTSSPS LHSRSPSISN MAALSRAHSP ALGVHSFSGV QRFNISSHNQ SPKRHSISHS PNSNSNGSFL APET EPIVP ELCIDHLWTE TITNIREKNS QASKVFITSD LCGQKFLCFL VESQLQLRCV KFQESNDKTQ LIFGSVTNIP AKDAA PVEK IDTMLVLEGS GNLVLYTGVV RVGKVFIPGL PAPSLTMSNT MPRPSTPLDG VSTPKPLSKL LGSLDEVVLL SPVPEL RDS SKLHDSLYNE DCTFQQLGTY IHSIRDPVHN RVTLELSNGS MVRITIPEIA TSELVQTCLQ AIKFILPKEI AVQMLVK WY NVHSAPGGPS YHSEWNLFVT CLMNMMGYNT DRLAWTRNFD FEGSLSPVIA PKKARPSETG SDDDWEYLLN SDYHQNVE S HLLNRSLCLS PSEASQMKDE DFSQNLSLDS STLLFTHIPA IFFVLHLVYE ELKLNTLMGE GICSLVELLV QLARDLKLG PYVDHYYRDY PTLVRTTGQV CTIDPGQTGF MHHPSFFTSE PPSIYQWVSS CLKGEGMPPY PYLPGICERS RLVVLSIALY ILGDESLVS DESSQYLTRI TIAPQKLQVE QEENRFSFRH STSVSSLAER LVVWMTNVGF TLRDLETLPF GIALPIRDAI Y HCREQPAS DWPEAVCLLI GRQDLSKQAC EGNLPKGKSV LSSDVPSGTE TEEEDDGMND MNHEVMSLIW SEDLRVQDVR RL LQSAHPV RVNVVQYPEL SDHEFIEEKE NRLLQLCQRT MALPVGRGMF TLFSYHPVPT EPLPIPKLNL TGRAPPRNTT VDL NSGNID VPPNMTSWAS FHNGVAAGLK IAPASQIDSA WIVYNKPKHA ELANEYAGFL MALGLNGHLT KLATLNIHDY LTKG HEMTS IGLLLGVSAA KLGTMDMSIT RLLSIHIPAL LPPTSTELDV PHNVQVAAVV GIGLVYQGTA HRHTAEVLLA EIGRP PGPE MEYCTDRESY SLAAGLALGM VCLGHGSNLI GMSDLNVPEQ LYQYMVGGHR RFQTGMHREK HKSPSYQIKE GDTINV DVT CPGATLALAM IYLKTNNRSI ADWLRAPDTM YLLDFVKPEF LLLRTLARCL ILWDDILPNS KWVDSNVPQI IRENSIS LS EIELPCSEDL NLETLSQAHV YIIAGACLSL GFRFAGSENL SAFNCLHKFA KDFMTYLSAP NASVTGPHNL ETCLSVVL L SLAMVMAGSG NLKVLQLCRF LHMKTGGEMN YGFHLAHHMA LGLLFLGGGR YSLSTSNSSI AALLCALYPH FPAHSTDNR YHLQALRHLY VLAAEPRLLV PVDVDTNTPC YALLEVTYKG TQWYEQTKEE LMAPTLLPEL HLLKQIKVKG PRYWELLIDL SKGTQHLKS ILSKDGVLYV KLRAGQLSYK EDPMGWQSLL AQTVANRNSE ARAFKPETIS AFTSDPALLS FAEYFCKPTV N MGQKQEIL DLFSSVLYEC VTQETPEMLP AYIAMDQAIR RLGRREMSET SELWQIKLVL EFFSSRSHQE RLQNHPKRGL FM NSEFLPV VKCTIDNTLD QWLQVGGDMC VHAYLSGQPL EESQLSMLAC FLVYHSVPAP QHLPPIGLEG STSFAELLFK FKQ LKMPVR ALLRLAPLLL GNPQPMVM

UniProtKB: Anaphase-promoting complex subunit 1

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Macromolecule #4: Anaphase-promoting complex subunit 2

MacromoleculeName: Anaphase-promoting complex subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.938977 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAAVVVAEG DSDSRPGQEL LVAWNTVSTG LVPPAALGLV SSRTSGAVPP KEEELRAAVE VLRGHGLHSV LEEWFVEVLQ NDLQANISP EFWNAISQCE NSADEPQCLL LLLDAFGLLE SRLDPYLRSL ELLEKWTRLG LLMGTGAQGL REEVHTMLRG V LFFSTPRT ...String:
MAAAVVVAEG DSDSRPGQEL LVAWNTVSTG LVPPAALGLV SSRTSGAVPP KEEELRAAVE VLRGHGLHSV LEEWFVEVLQ NDLQANISP EFWNAISQCE NSADEPQCLL LLLDAFGLLE SRLDPYLRSL ELLEKWTRLG LLMGTGAQGL REEVHTMLRG V LFFSTPRT FQEMIQRLYG CFLRVYMQSK RKGEGGTDPE LEGELDSRYA RRRYYRLLQS PLCAGCSSDK QQCWCRQALE QF HQLSQVL HRLSLLERVS AEAVTTTLHQ VTRERMEDRC RGEYERSFLR EFHKWIERVV GWLGKVFLQD GPARPASPEA GNT LRRWRC HVQRFFYRIY ASLRIEELFS IVRDFPDSRP AIEDLKYCLE RTDQRQQLLV SLKAALETRL LHPGVNTCDI ITLY ISAIK ALRVLDPSMV ILEVACEPIR RYLRTREDTV RQIVAGLTGD SDGTGDLAVE LSKTDPASLE TGQDSEDDSG EPEDW VPDP VDADPGKSSS KRRSSDIISL LVSIYGSKDL FINEYRSLLA DRLLHQFSFS PEREIRNVEL LKLRFGEAPM HFCEVM LKD MADSRRINAN IREEDEKRPA EEQPPFGVYA VILSSEFWPP FKDEKLEVPE DIRAALEAYC KKYEQLKAMR TLSWKHT LG LVTMDVELAD RTLSVAVTPV QAVILLYFQD QASWTLEELS KAVKMPVALL RRRMSVWLQQ GVLREEPPGT FSVIEEER P QDRDNMVLID SDDESDSGMA SQADQKEEEL LLFWTYIQAM LTNLESLSLD RIYNMLRMFV VTGPALAEID LQELQGYLQ KKVRDQQLVY SAGVYRLPKN CS

UniProtKB: Anaphase-promoting complex subunit 2

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Macromolecule #5: Anaphase-promoting complex subunit 4

MacromoleculeName: Anaphase-promoting complex subunit 4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.01407 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MLRFPTCFPS FRVVGEKQLP QEIIFLVWSP KRDLIALANT AGEVLLHRLA SFHRVWSFPP NENTGKEVTC LAWRPDGKLL AFALADTKK IVLCDVEKPE SLHSFSVEAP VSCMHWMEVT VESSVLTSFY NAEDESNLLL PKLPTLPKNY SNTSKIFSEE N SDEIIKLL ...String:
MLRFPTCFPS FRVVGEKQLP QEIIFLVWSP KRDLIALANT AGEVLLHRLA SFHRVWSFPP NENTGKEVTC LAWRPDGKLL AFALADTKK IVLCDVEKPE SLHSFSVEAP VSCMHWMEVT VESSVLTSFY NAEDESNLLL PKLPTLPKNY SNTSKIFSEE N SDEIIKLL GDVRLNILVL GGSSGFIELY AYGMFKIARV TGIAGTCLAL CLSSDLKSLS VVTEVSTNGA SEVSYFQLET NL LYSFLPE VTRMARKFTH ISALLQYINL SLTCMCEAWE EILMQMDSRL TKFVQEKNTT TSVQDEFMHL LLWGKASAEL QTL LMNQLT VKGLKKLGQS IESSYSSIQK LVISHLQSGS ESLLYHLSEL KGMASWKQKY EPLGLDAAGI EEAITAVGSF ILKA NELLQ VIDSSMKNFK AFFRWLYVAM LRMTEDHVLP ELNKMTQKDI TFVAEFLTEH FNEAPDLYNR KGKYFNVERV GQYLK DEDD DLVSPPNTEG NQWYDFLQNS SHLKESPLLF PYYPRKSLHF VKRRMENIID QCLQKPADVI GKSMNQAICI PLYRDT RSE DSTRRLFKFP FLWNNKTSNL HYLLFTILED SLYKMCILRR HTDISQSVSN GLIAIKFGSF TYATTEKVRR SIYSCLD AQ FYDDETVTVV LKDTVGREGR DRLLVQLPLS LVYNSEDSAE YQFTGTYSTR LDEQCSAIPT RTMHFEKHWR LLESMKAQ Y VAGNGFRKVS CVLSSNLRHV RVFEMDIDDE WELDESSDEE EEASNKPVKI KEEVLSESEA ENQQAGAAAL APEIVIKVE KLDPELDSEN LYFQ

UniProtKB: Anaphase-promoting complex subunit 4

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Macromolecule #6: Anaphase-promoting complex subunit 5

MacromoleculeName: Anaphase-promoting complex subunit 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.179766 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASVHESLYF NPMMTNGVVH ANVFGIKDWV TPYKIAVLVL LNEMSRTGEG AVSLMERRRL NQLLLPLLQG PDITLSKLYK LIEESCPQL ANSVQIRIKL MAEGELKDME QFFDDLSDSF SGTEPEVHKT SVVGLFLRHM ILAYSKLSFS QVFKLYTALQ Q YFQNGEKK ...String:
MASVHESLYF NPMMTNGVVH ANVFGIKDWV TPYKIAVLVL LNEMSRTGEG AVSLMERRRL NQLLLPLLQG PDITLSKLYK LIEESCPQL ANSVQIRIKL MAEGELKDME QFFDDLSDSF SGTEPEVHKT SVVGLFLRHM ILAYSKLSFS QVFKLYTALQ Q YFQNGEKK TVEDADMELT SRDEGERKME KEELDVSVRE EEVSCSGPLS QKQAEFFLSQ QASLLKNDET KALTPASLQK EL NNLLKFN PDFAEAHYLS YLNNLRVQDV FSSTHSLLHY FDRLILTGAE SKSNGEEGYG RSLRYAALNL AALHCRFGHY QQA ELALQE AIRIAQESND HVCLQHCLSW LYVLGQKRSD SYVLLEHSVK KAVHFGLPYL ASLGIQSLVQ QRAFAGKTAN KLMD ALKDS DLLHWKHSLS ELIDISIAQK TAIWRLYGRS TMALQQAQML LSMNSLEAVN AGVQQNNTES FAVALCHLAE LHAEQ GCFA AASEVLKHLK ERFPPNSQHA QLWMLCDQKI QFDRAMNDGK YHLADSLVTG ITALNSIEGV YRKAVVLQAQ NQMSEA HKL LQKLLVHCQK LKNTEMVISV LLSVAELYWR SSSPTIALPM LLQALALSKE YRLQYLASET VLNLAFAQLI LGIPEQA LS LLHMAIEPIL ADGAILDKGR AMFLVAKCQV ASAASYDQPK KAEALEAAIE NLNEAKNYFA KVDCKERIRD VVYFQARL Y HTLGKTQERN RCAMLFRQLH QELPSHGVPL INHL

UniProtKB: Anaphase-promoting complex subunit 5

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Macromolecule #7: F-box only protein 5

MacromoleculeName: F-box only protein 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.227488 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSRRPCSCAL RPPRCSCSAS PSAVTAAGRP RPSDSCKEES STLSVKMKCD FNCNHVHSGL KLVKPDDIGR LVSYTPAYLE GSCKDCIKD YERLSCIGSP IVSPRIVQLE TESKRLHNKE NQHVQQTLNS TNEIEALETS RLYEDSGYSS FSLQSGLSEH E EGSLLEEN ...String:
MSRRPCSCAL RPPRCSCSAS PSAVTAAGRP RPSDSCKEES STLSVKMKCD FNCNHVHSGL KLVKPDDIGR LVSYTPAYLE GSCKDCIKD YERLSCIGSP IVSPRIVQLE TESKRLHNKE NQHVQQTLNS TNEIEALETS RLYEDSGYSS FSLQSGLSEH E EGSLLEEN FGDSLQSCLL QIQSPDQYPN KNLLPVLHFE KVVCSTLKKN AKRNPKVDRE MLKEIIARGN FRLQNIIGRK MG LECVDIL SELFRRGLRH VLATILAQLS DMDLINVSKV STTWKKILED DKGAFQLYSK AIQRVTENNN KFSPHASTRE YVM FRTPLA SVQKSAAQTS LKKDAQTKLS NQGDQKGSTY SRHNEFSEVA KTLKKNESLK ACIRCNSPAK YDCYLQRATC KREG CGFDY CTKCLCNYHT TKDCSDGKLL KASCKIGPLP GTKKSKKNLR RL

UniProtKB: F-box only protein 5

+
Macromolecule #8: Cell division cycle protein 16 homolog

MacromoleculeName: Cell division cycle protein 16 homolog / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.747516 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNLERLRKRV RQYLDQQQYQ SALFWADKVA SLSREEPQDI YWLAQCLYLT AQYHRAAHAL RSRKLDKLYE ACRYLAARCH YAAKEHQQA LDVLDMEEPI NKRLFEKYLK DESGFKDPSS DWEMSQSSIK SSICLLRGKI YDALDNRTLA TYSYKEALKL D VYCFEAFD ...String:
MNLERLRKRV RQYLDQQQYQ SALFWADKVA SLSREEPQDI YWLAQCLYLT AQYHRAAHAL RSRKLDKLYE ACRYLAARCH YAAKEHQQA LDVLDMEEPI NKRLFEKYLK DESGFKDPSS DWEMSQSSIK SSICLLRGKI YDALDNRTLA TYSYKEALKL D VYCFEAFD LLTSHHMLTA QEEKELLESL PLSKLCNEEQ ELLRFLFENK LKKYNKPSET VIPESVDGLQ ENLDVVVSLA ER HYYNCDF KMCYKLTSVV MEKDPFHASC LPVHIGTLVE LNKANELFYL SHKLVDLYPS NPVSWFAVGC YYLMVGHKNE HAR RYLSKA TTLEKTYGPA WIAYGHSFAV ESEHDQAMAA YFTAAQLMKG CHLPMLYIGL EYGLTNNSKL AERFFSQALS IAPE DPFVM HEVGVVAFQN GEWKTAEKWF LDALEKIKAI GNEVTVDKWE PLLNNLGHVC RKLKKYAEAL DYHRQALVLI PQNAS TYSA IGYIHSLMGN FENAVDYFHT ALGLRRDDTF SVTMLGHCIE MYIGDSEAYI GADIKDKLKC YDFDVHTMKT LKNIIS PPW DFREFEVEKQ TAEETGLTPL ETSRKTPDSR PSLEETFEIE MNESDMMLET SMSDHST

UniProtKB: Cell division cycle protein 16 homolog

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Macromolecule #9: Anaphase-promoting complex subunit CDC26

MacromoleculeName: Anaphase-promoting complex subunit CDC26 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.793999 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MLRRKPTRLE LKLDDIEEFE NIRKDLETRK KQKEDVEVVG GSDGEGAIGL SSDPKSREQM INDRIGYKPQ PKPNNRSSQF GSLEF

UniProtKB: Anaphase-promoting complex subunit CDC26

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Macromolecule #10: Anaphase-promoting complex subunit 13

MacromoleculeName: Anaphase-promoting complex subunit 13 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.528309 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MDSEVQRDGR ILDLIDDAWR EDKLPYEDVA IPLNELPEPE QDNGGTTESV KEQEMKWTDL ALQYLHENVP PIGN

UniProtKB: Anaphase-promoting complex subunit 13

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Macromolecule #11: Anaphase-promoting complex subunit 16

MacromoleculeName: Anaphase-promoting complex subunit 16 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.677995 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAASSSSSSA GGVSGSSVTG SGFSVSDLAP PRKALFTYPK GAGEMLEDGS ERFLCESVFS YQVASTLKQV KHDQQVARME KLAGLVEEL EADEWRFKPI EQLLGFTPSS G

UniProtKB: Anaphase-promoting complex subunit 16

+
Macromolecule #12: Cell division cycle protein 27 homolog

MacromoleculeName: Cell division cycle protein 27 homolog / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.973125 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTVLQEPVQA AIWQALNHYA YRDAVFLAER LYAEVHSEEA LFLLATCYYR SGKAYKAYRL LKGHSCTTPQ CKYLLAKCCV DLSKLAEGE QILSGGVFNK QKSHDDIVTE FGDSACFTLS LLGHVYCKTD RLAKGSECYQ KSLSLNPFLW SPFESLCEIG E KPDPDQTF ...String:
MTVLQEPVQA AIWQALNHYA YRDAVFLAER LYAEVHSEEA LFLLATCYYR SGKAYKAYRL LKGHSCTTPQ CKYLLAKCCV DLSKLAEGE QILSGGVFNK QKSHDDIVTE FGDSACFTLS LLGHVYCKTD RLAKGSECYQ KSLSLNPFLW SPFESLCEIG E KPDPDQTF KFTSLQNFSN CLPNSCTTQV PNHSLSHRQP ETVLTETPQD TIELNRLNLE SSNSKYSLNT DSSVSYIDSA VI SPDTVPL GTGTSILSKQ VQNKPKTGRS LLGGPAALSP LTPSFGILPL ETPSPGDGSY LQNYTNTPPV IDVPSTGAPS KKS VARIGQ TGTKSVFSQS GNSREVTPIL AQTQSSGPQT STTPQVLSPT ITSPPNALPR RSSRLFTSDS STTKENSKKL KMKF PPKIP NRKTKSKTNK GGITQPNIND SLEITKLDSS IISEGKISTI TPQIQAFNLQ KAAAEGLMSL LREMGKGYLA LCSYN CKEA INILSHLPSH HYNTGWVLCQ IGRAYFELSE YMQAERIFSE VRRIENYRVE GMEIYSTTLW HLQKDVALSV LSKDLT DMD KNSPEAWCAA GNCFSLQREH DIAIKFFQRA IQVDPNYAYA YTLLGHEFVL TEELDKALAC FRNAIRVNPR HYNAWYG LG MIYYKQEKFS LAEMHFQKAL DINPQSSVLL CHIGVVQHAL KKSEKALDTL NKAIVIDPKN PLCKFHRASV LFANEKYK S ALQELEELKQ IVPKESLVYF LIGKVYKKLG QTHLALMNFS WAMDLDPKGA NNQIKEAIDK RYLPDDEEPI TQEEQIMGT DESQESSMTD ADDTQLHAAE SDEF

UniProtKB: Cell division cycle protein 27 homolog

+
Macromolecule #13: Anaphase-promoting complex subunit 7

MacromoleculeName: Anaphase-promoting complex subunit 7 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.929367 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDPGDAAILE SSLRILYRLF ESVLPPLPAA LQSRMNVIDH VRDMAAAGLH SNVRLLSSLL LTMSNNNPEL FSPPQKYQLL VYHADSLFH DKEYRNAVSK YTMALQQKKA LSKTSKVRPS TGNSASTPQS QCLPSEIEVK YKMAECYTML KQDKDAIAIL D GIPSRQRT ...String:
MDPGDAAILE SSLRILYRLF ESVLPPLPAA LQSRMNVIDH VRDMAAAGLH SNVRLLSSLL LTMSNNNPEL FSPPQKYQLL VYHADSLFH DKEYRNAVSK YTMALQQKKA LSKTSKVRPS TGNSASTPQS QCLPSEIEVK YKMAECYTML KQDKDAIAIL D GIPSRQRT PKINMMLANL YKKAGQERPS VTSYKEVLRQ CPLALDAILG LLSLSVKGAE VASMTMNVIQ TVPNLDWLSV WI KAYAFVH TGDNSRAIST ICSLEKKSLL RDNVDLLGSL ADLYFRAGDN KNSVLKFEQA QMLDPYLIKG MDVYGYLLAR EGR LEDVEN LGCRLFNISD QHAEPWVVSG CHSFYSKRYS RALYLGAKAI QLNSNSVQAL LLKGAALRNM GRVQEAIIHF REAI RLAPC RLDCYEGLIE CYLASNSIRE AMVMANNVYK TLGANAQTLT LLATVCLEDP VTQEKAKTLL DKALTQRPDY IKAVV KKAE LLSREQKYED GIALLRNALA NQSDCVLHRI LGDFLVAVNE YQEAMDQYSI ALSLDPNDQK SLEGMQKMEK EESPTD ATQ EEDVDDMEGS GEEGDLEGSD SEAAQWADQE QWFGMQ

UniProtKB: Anaphase-promoting complex subunit 7

+
Macromolecule #14: Cell division cycle protein 23 homolog

MacromoleculeName: Cell division cycle protein 23 homolog / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.921031 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAASTSMVPV AVTAAVAPVL SINSDFSDLR EIKKQLLLIA GLTRERGLLH SSKWSAELAF SLPALPLAEL QPPPPITEED AQDMDAYTL AKAYFDVKEY DRAAHFLHGC NSKKAYFLYM YSRYLSGEKK KDDETVDSLG PLEKGQVKNE ALRELRVELS K KHQARELD ...String:
MAASTSMVPV AVTAAVAPVL SINSDFSDLR EIKKQLLLIA GLTRERGLLH SSKWSAELAF SLPALPLAEL QPPPPITEED AQDMDAYTL AKAYFDVKEY DRAAHFLHGC NSKKAYFLYM YSRYLSGEKK KDDETVDSLG PLEKGQVKNE ALRELRVELS K KHQARELD GFGLYLYGVV LRKLDLVKEA IDVFVEATHV LPLHWGAWLE LCNLITDKEM LKFLSLPDTW MKEFFLAHIY TE LQLIEEA LQKYQNLIDV GFSKSSYIVS QIAVAYHNIR DIDKALSIFN ELRKQDPYRI ENMDTFSNLL YVRSMKSELS YLA HNLCEI DKYRVETCCV IGNYYSLRSQ HEKAALYFQR ALKLNPRYLG AWTLMGHEYM EMKNTSAAIQ AYRHAIEVNK RDYR AWYGL GQTYEILKMP FYCLYYYRRA HQLRPNDSRM LVALGECYEK LNQLVEAKKC YWRAYAVGDV EKMALVKLAK LHEQL TESE QAAQCYIKYI QDIYSCGEIV EHLEESTAFR YLAQYYFKCK LWDEASTCAQ KCCAFNDTRE EGKALLRQIL QLRNQG ETP TTEVPAPFFL PASLSANNTP TRRVSPLNLS SVTP

UniProtKB: Cell division cycle protein 23 homolog

+
Macromolecule #15: Fizzy-related protein homolog

MacromoleculeName: Fizzy-related protein homolog / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.253207 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDQDYERRLL RQIVIQNENT MPRVTEMRRT LTPASSPVSS PSKHGDRFIP SRAGANWSVN FHRINENEKS PSQNRKAKDA TSDNGKDGL AYSALLKNEL LGAGIEKVQD PQTEDRRLQP STPEKKGLFT YSLSTKRSSP DDGNDVSPYS LSPVSNKSQK L LRSPRKPT ...String:
MDQDYERRLL RQIVIQNENT MPRVTEMRRT LTPASSPVSS PSKHGDRFIP SRAGANWSVN FHRINENEKS PSQNRKAKDA TSDNGKDGL AYSALLKNEL LGAGIEKVQD PQTEDRRLQP STPEKKGLFT YSLSTKRSSP DDGNDVSPYS LSPVSNKSQK L LRSPRKPT RKISKIPFKV LDAPELQDDF YLNLVDWSSL NVLSVGLGTC VYLWSACTSQ VTRLCDLSVE GDSVTSVGWS ER GNLVAVG THKGFVQIWD AAAGKKLSML EGHTARVGAL AWNAEQLSSG SRDRMILQRD IRTPPLQSER RLQGHRQEVC GLK WSTDHQ LLASGGNDNK LLVWNHSSLS PVQQYTEHLA AVKAIAWSPH QHGLLASGGG TADRCIRFWN TLTGQPLQCI DTGS QVCNL AWSKHANELV STHGYSQNQI LVWKYPSLTQ VAKLTGHSYR VLYLAMSPDG EAIVTGAGDE TLRFWNVFSK TRSTK VKWE SVSVLNLFTR IR

UniProtKB: Fizzy-related protein homolog

+
Macromolecule #16: Anaphase-promoting complex subunit 11

MacromoleculeName: Anaphase-promoting complex subunit 11 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.854647 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MKVKIKCWNG VATWLWVAND ENCGICRMAF NGCCPDCKVP GDDCPLVWGQ CSHCFHMHCI LKWLHAQQVQ QHCPMCRQEW KFKE

UniProtKB: Anaphase-promoting complex subunit 11

+
Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 6 / 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

Concentration0.1 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHepes2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
200.0 mMNaClsodium chloride
2.0 mMDTTDithiothreitol
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 50
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 8297 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1800000 / Details: The particles were automatically selected
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.14.2) / Software - details: Non-uniform refinement was used / Number images used: 364331
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14.2)
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 3.1 beta)

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Atomic model buiding 1

Initial modelPDB ID:

4ui9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 80
Output model

PDB-9gaw:
High-resolution structure of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-activator Cdh1

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