[English] 日本語
Yorodumi
- EMDB-15199: S. cerevisiae apo unphosphorylated APC/C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15199
TitleS. cerevisiae apo unphosphorylated APC/C
Map dataApo unphosphorylated S. cerevisiae APC/C
Sample
  • Complex: Anaphase promoting complex/cyclosome (APC/C)
    • Complex: unphosphorylated apo APC/C complex
      • Protein or peptide: x 13 types
  • Ligand: x 1 types
KeywordsAPC/C / ubiqutiniation / D-box / Cdh1 / CELL CYCLE
Function / homology
Function and homology information


anaphase-promoting complex assembly / negative regulation of anaphase-promoting complex-dependent catabolic process / : / deactivation of mitotic spindle assembly checkpoint / ascospore wall assembly / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition ...anaphase-promoting complex assembly / negative regulation of anaphase-promoting complex-dependent catabolic process / : / deactivation of mitotic spindle assembly checkpoint / ascospore wall assembly / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / metaphase/anaphase transition of mitotic cell cycle / Antigen processing: Ubiquitination & Proteasome degradation / exit from mitosis / protein K11-linked ubiquitination / positive regulation of protein autoubiquitination / reciprocal meiotic recombination / regulation of mitotic metaphase/anaphase transition / ubiquitin ligase inhibitor activity / mitotic sister chromatid segregation / cullin family protein binding / ligase activity / enzyme regulator activity / negative regulation of DNA-templated DNA replication initiation / regulation of mitotic cell cycle / cyclin binding / nuclear periphery / kinetochore / spindle pole / ubiquitin protein ligase activity / chromatin organization / ubiquitin-dependent protein catabolic process / molecular adaptor activity / protein ubiquitination / cell cycle / cell division / ubiquitin protein ligase binding / mitochondrion / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Anaphase-promoting complex subunit 15/mnd2 / Anaphase-promoting complex subunit Mnd2 / Anaphase-promoting complex, subunit 9 / Apc15p protein / Anaphase-promoting complex subunit 9 / Cdc23 / Apc13 / Anaphase promoting complex subunit 8 / Cdc23 / Apc13p protein / Anaphase-promoting complex subunit 4 ...Anaphase-promoting complex subunit 15/mnd2 / Anaphase-promoting complex subunit Mnd2 / Anaphase-promoting complex, subunit 9 / Apc15p protein / Anaphase-promoting complex subunit 9 / 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 / Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Anaphase-promoting complex, cyclosome, subunit 3 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Tetratricopeptide repeat 1 / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Anaphase-promoting complex subunit CDC16 / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit CDC23 / Anaphase-promoting complex subunit CDC27 / Anaphase-promoting complex subunit MND2 / Anaphase-promoting complex subunit DOC1 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 9 ...Anaphase-promoting complex subunit CDC16 / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit CDC23 / Anaphase-promoting complex subunit CDC27 / Anaphase-promoting complex subunit MND2 / Anaphase-promoting complex subunit DOC1 / Anaphase-promoting complex subunit 1 / Anaphase-promoting complex subunit 4 / Anaphase-promoting complex subunit 5 / Anaphase-promoting complex subunit 9 / Anaphase-promoting complex subunit 11 / Anaphase-promoting complex subunit SWM1 / Anaphase-promoting complex subunit 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsBarford D / Fernandez-Vazquez E / Zhang Z / Yang J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of the S. cerevisiae APC/C-Cdh1 complex and comparison to apo unphosphorylated and phosphorylated states
Authors: Barford D / Fernandez-Vazquez E / Zhang Z / Yang J
History
DepositionJun 16, 2022-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15199.png

Downloads & links

-
Map

FileDownload / File: emd_15199.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationApo unphosphorylated S. cerevisiae APC/C
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.10617933 - 0.21401817
Average (Standard dev.)0.0012142567 (±0.00827269)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Halk map2

Fileemd_15199_half_map_1.map
AnnotationHalk map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map1

Fileemd_15199_half_map_2.map
AnnotationHalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Anaphase promoting complex/cyclosome (APC/C)

EntireName: Anaphase promoting complex/cyclosome (APC/C)
Components
  • Complex: Anaphase promoting complex/cyclosome (APC/C)
    • Complex: unphosphorylated apo APC/C complex
      • Protein or peptide: Anaphase-promoting complex subunit CDC27
      • Protein or peptide: Anaphase-promoting complex subunit CDC16
      • Protein or peptide: Anaphase-promoting complex subunit CDC26
      • Protein or peptide: Anaphase-promoting complex subunit 9
      • Protein or peptide: Anaphase-promoting complex subunit 2
      • Protein or peptide: Anaphase-promoting complex subunit 11
      • Protein or peptide: Anaphase-promoting complex subunit 1
      • Protein or peptide: Anaphase-promoting complex subunit 5
      • Protein or peptide: Anaphase-promoting complex subunit CDC23
      • Protein or peptide: Anaphase-promoting complex subunit SWM1
      • Protein or peptide: Anaphase-promoting complex subunit MND2
      • Protein or peptide: Anaphase-promoting complex subunit 4
      • Protein or peptide: Anaphase-promoting complex subunit DOC1
  • Ligand: ZINC ION

+
Supramolecule #1: Anaphase promoting complex/cyclosome (APC/C)

SupramoleculeName: Anaphase promoting complex/cyclosome (APC/C) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Details: Apo unphosphorylated anaphase promoting complex/cyclosome (APC/C)
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.127 MDa

+
Supramolecule #2: unphosphorylated apo APC/C complex

SupramoleculeName: unphosphorylated apo APC/C complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#13
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: Anaphase-promoting complex subunit CDC27

MacromoleculeName: Anaphase-promoting complex subunit CDC27 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 85.487391 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAVNPELAPF TLSRGIPSFD DQALSTIIQL QDCIQQAIQQ LNYSTAEFLA ELLYAECSIL DKSSVYWSDA VYLYALSLFL NKSYHTAFQ ISKEFKEYHL GIAYIFGRCA LQLSQGVNEA ILTLLSIINV FSSNSSNTRI NMVLNSNLVH IPDLATLNCL L GNLYMKLD ...String:
MAVNPELAPF TLSRGIPSFD DQALSTIIQL QDCIQQAIQQ LNYSTAEFLA ELLYAECSIL DKSSVYWSDA VYLYALSLFL NKSYHTAFQ ISKEFKEYHL GIAYIFGRCA LQLSQGVNEA ILTLLSIINV FSSNSSNTRI NMVLNSNLVH IPDLATLNCL L GNLYMKLD HSKEGAFYHS EALAINPYLW ESYEAICKMR ATVDLKRVFF DIAGKKSNSH NNNAASSFPS TSLSHFEPRS QP SLYSKTN KNGNNNINNN VNTLFQSSNS PPSTSASSFS SIQHFSRSQQ QQANTSIRTC QNKNTQTPKN PAINSKTSSA LPN NISMNL VSPSSKQPTI SSLAKVYNRN KLLTTPPSKL LNNDRNHQNN NNNNNNNNNN NNNNNNNNNN NNIINKTTFK TPRN LYSST GRLTTSKKNP RSLIISNSIL TSDYSITLPE IMYNFALILR SSSQYNSFKA IRLFESQIPS HIKDTMPWCL VQLGK LHFE IINYDMSLKY FNRLKDLQPA RVKDMEIFST LLWHLHDKVK SSNLANGLMD TMPNKPETWC CIGNLLSLQK DHDAAI KAF EKATQLDPNF AYAYTLQGHE HSSNDSSDSA KTCYRKALAC DPQHYNAYYG LGTSAMKLGQ YEEALLYFEK ARSINPV NV VLICCCGGSL EKLGYKEKAL QYYELACHLQ PTSSLSKYKM GQLLYSMTRY NVALQTFEEL VKLVPDDATA HYLLGQTY R IVGRKKDAIK ELTVAMNLDP KGNQVIIDEL QKCHMQE

UniProtKB: Anaphase-promoting complex subunit CDC27

+
Macromolecule #2: Anaphase-promoting complex subunit CDC16

MacromoleculeName: Anaphase-promoting complex subunit CDC16 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 96.282266 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKFCLYCCHC YIVICGKATH YYKSSKATSN LKSSNRVLMR NPMSPSEQHS QHNSTLAASP FVSNVSAART QQSLPTDAQN DRLQQPWNR TNTATSPYQS LANSPLIQKL QANIMTPHQP SANSNSNSNS ITGNVVNDNN LLASMSKNSM FGSTIPSTLR K VSLQREYK ...String:
MKFCLYCCHC YIVICGKATH YYKSSKATSN LKSSNRVLMR NPMSPSEQHS QHNSTLAASP FVSNVSAART QQSLPTDAQN DRLQQPWNR TNTATSPYQS LANSPLIQKL QANIMTPHQP SANSNSNSNS ITGNVVNDNN LLASMSKNSM FGSTIPSTLR K VSLQREYK DSVDGVVRDE DNDEDVHNNG DAAANANNDR ESKLGHNGPL TTTTLTTTTT ATQLDVSELS AIERLRLWRF DA LMQHMYR TAEYIADKVY NISNDPDDAF WLGQVYYNNN QYVRAVELIT RNNLDGVNIL CRYLLGLSFV KLQRFDDALD VIG EYNPFS EDPSTTAANT MSNNGNNSNT SQPVTDGGIK MESSLCFLRG KIYFAQNNFN KARDAFREAI LVDIKNFEAF EMLL SKNLL TPQEEWDLFD SLDFKEFGED KEIMKNLYKI NLSKYINTED ITKSNEILAK DYKLADNVDV VRSKVDICYT QCKFN ECLE LCETVLENDE FNTNILPAYI GCLYELSNKN KLFLLSHRLA ETFPKSAITW FSVATYYMSL DRISEAQKYY SKSSIL DPS FAAAWLGFAH TYALEGEQDQ ALTAYSTASR FFPGMHLPKL FLGMQFMAMN SLNLAESYFV LAYDICPNDP LVLNEMG VM YFKKNEFVKA KKYLKKALEV VKDLDPSSRT TISIQLNLGH TYRKLNENEI AIKCFRCVLE KNDKNSEIHC SLGYLYLK T KKLQKAIDHL HKSLYLKPNN SSATALLKNA LELNVTLSLD ASHPLIDKSN LMSQASKDKA SLNKKRSSLT YDPVNMAKR LRTQKEIFDQ NNKALRKGGH DSKTGSNNAD DDFDADMELE KSSIPENLYF

UniProtKB: Anaphase-promoting complex subunit CDC16

+
Macromolecule #3: Anaphase-promoting complex subunit CDC26

MacromoleculeName: Anaphase-promoting complex subunit CDC26 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.09686 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MIRRAPTTLQ LSHDDVTSLI DDLNEQKLKQ QLNIEKTKYF QGKNGGSLHS NTDFQDTSQN IEDNNNDNDN DIDEDDDMSS YNDKAASVA HTRVLNSLHL STDSNTAHET SNANDNHNPF YIREE

UniProtKB: Anaphase-promoting complex subunit CDC26

+
Macromolecule #4: Anaphase-promoting complex subunit 9

MacromoleculeName: Anaphase-promoting complex subunit 9 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 30.901439 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNQNGDKNEG KLFQLPSLPP WKTPRFNKAN FNNFTTPLRK RSTRVINDDS MPITGEVLEE RTADDLYGIN MDVDEVDYLN TLSHIEEEK QYDYSPFCER NTLRESRIDS FLKAERAAHC LVFHKVGHLD GIDSYRPDID IMCGEEANKY DSANPEGNGS M LLESVPGC ...String:
MNQNGDKNEG KLFQLPSLPP WKTPRFNKAN FNNFTTPLRK RSTRVINDDS MPITGEVLEE RTADDLYGIN MDVDEVDYLN TLSHIEEEK QYDYSPFCER NTLRESRIDS FLKAERAAHC LVFHKVGHLD GIDSYRPDID IMCGEEANKY DSANPEGNGS M LLESVPGC NKEDLERLSR REFVTNSKPN MRRLDDIINH ETNALKSFWN DSGLVNSLQS HHLHEEYLLL QEELKNVYKI KC HDRVPIE SLRDKCRRHY SNEDSSFL

UniProtKB: Anaphase-promoting complex subunit 9

+
Macromolecule #5: Anaphase-promoting complex subunit 2

MacromoleculeName: Anaphase-promoting complex subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 100.09957 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSFQITPTRD LKVITDELQT LSSYIFHTNI VDDLNSLLTW MSPNDAKSNH QLRPPSLRIK NIIKVLFPNN ATTSPYSMIN TSQANNSIV NEGNTNKELQ LQLFSTLKEF YIFQVRYHFF LHFNNINYLK DIQRWENYYE FPLRYVPIFD VNVNDWALEL N SLRHYLLN ...String:
MSFQITPTRD LKVITDELQT LSSYIFHTNI VDDLNSLLTW MSPNDAKSNH QLRPPSLRIK NIIKVLFPNN ATTSPYSMIN TSQANNSIV NEGNTNKELQ LQLFSTLKEF YIFQVRYHFF LHFNNINYLK DIQRWENYYE FPLRYVPIFD VNVNDWALEL N SLRHYLLN RNIKFKNNLR TRLDKLIMDD DFDLADNLIQ WLKSANGSLS STELIVNALY SKINKFCEDN MSRVWNKRFM IM ETFNKFI NQYWSQFSKL VGCPEDDHEL TTTVFNCFES NFLRIRTNEI FDICVLAYPD SKVTLLELRK IMKDFKDYTN IVT TFLSDF KKYILNPSVT TVDALLRYVK TIKAFLVLDP TGRCLHSITT FVKPYFQERK HLVNVLLYAM LDLPEEELKE KINF NVDMK ALLSLVDTLH DSDINQDTNI TKRDKNKKSP FLWNLKVKGK RELNKDLPIR HAMLYEHILN YYIAWVPEPN DMIPG NIKS SYIKTNLFEV LLDLFESREF FISEFRNLLT DRLFTLKFYT LDEKWTRCLK LIREKIVKFT ETSHSNYITN GILGLL ETT APAADADQSN LNSIDVMLWD IKCSEELCRK MHEVAGLDPI IFPKFISLLY WKYNCDTQGS NDLAFHLPID LERELQK YS DIYSQLKPGR KLQLCKDKGK VEIQLAFKDG RKLVLDVSLE QCSVINQFDS PNDEPICLSL EQLSESLNIA PPRLTHLL D FWIQKGVLLK ENGTYSVIEH SEMDFDQAQK TAPMEIENSN YELHNDSEIE RKYELTLQRS LPFIEGMLTN LGAMKLHKI HSFLKITVPK DWGYNRITLQ QLEGYLNTLA DEGRLKYIAN GSYEIVKNGH KNS

UniProtKB: Anaphase-promoting complex subunit 2

+
Macromolecule #6: Anaphase-promoting complex subunit 11

MacromoleculeName: Anaphase-promoting complex subunit 11 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
EC number: Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 18.887105 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MKVKINEVHS VFAWSWHIPS TSDEDAANND PIGNDEDEDV CGICRASYNG TCPSCKFPGD QCPLVIGLCH HNFHDHCIYR WLDTPTSKG LCPMCRQTFQ LQKGLAINDA HVQKFVEIVS RRREEMIEEG VAEEFVDFDE PIRQNTDNPI GRQQVDTILD E DFLLR

UniProtKB: Anaphase-promoting complex subunit 11

+
Macromolecule #7: Anaphase-promoting complex subunit 1

MacromoleculeName: Anaphase-promoting complex subunit 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 196.372766 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTSKPSTRND YLPRETHNGE YTGDSPEWQL QINITNKIGG INGDIWLSRD GRSVKWCIED QCLRQFTYNQ KIIKAGYIDF EKTPDCFVV VLSDIAHVYM LKNGGSTTVC FPFQIGNAFW YANGVILERE TSASFMDGGY DLKPIEFDLK HKYITLTDPM A PFGLISIT ...String:
MTSKPSTRND YLPRETHNGE YTGDSPEWQL QINITNKIGG INGDIWLSRD GRSVKWCIED QCLRQFTYNQ KIIKAGYIDF EKTPDCFVV VLSDIAHVYM LKNGGSTTVC FPFQIGNAFW YANGVILERE TSASFMDGGY DLKPIEFDLK HKYITLTDPM A PFGLISIT NTFKGGINSA SGNKTDILQD FQLVLFPSDK DKCIAVFLDR NSKVLRFYYS RILSSDQSRK GELTISSTKK TG LDAAGNS QKSGGISKDL RKFSHLTRRS TSINSNSHDF NAAERVLSGN VGNASGRTDI FALPSSCSRR SLSATLDRMG NNI APTNRA APSGFFDSSS ANTATHSNIT PVSQPMQQQQ QEYLNQTATS SKDIVLTEIS SLKLPDDIIF TSRRLSSILS KLKF LSLRF ERREGLLIFH EPTHFCKIWL IDLLPDVLDS IPFKIYGNSP QNMIRLENLK LKEPSRIQAM YIHELLESCL ILVSE GQNK EEYKACLYDP FVKITSPSKN ISEELTKQNS LPSLQKLFPY PETSFTKLCF EAVKYITSPA FNISFIFLWQ SAYSIL LSR ANDDVVGGLK MEHDAFSLVL SLLILPIPSS SAQEYQEYKE IYERDLFQHL KQDSEITSSV LPRIVIGLHL IREEYSL NV LCRNEHALLG QFLRFATAAM GWPDLWQSYY VPKMDSESKT FLHPREQNST FFHPLDEPPS ITKSLYSITE NSSIPLCP F ISFSRLVATD TQVELRITPR SFKILGLYEL VHSPNFLPDY VLGILSSFKV DKDELQTYPL GILVPLQNIL KILEDKLSE VRDNLELLDR ADLQRCSAII NSIRSDSKEV LKRGQRDSYM LCKVPLAKNR SSLSKKPSDI YSILSEIVKS ASQVPLDGSA MRMSNIQDD EDIDEGRSLK LNAGLIFSED KRFTHVVSLL AYYRPTKTQF FTTKTEYAQI LAQKKYFAKI MALRTCTNGV G WGAVAYAT EKPISTQKWV IQPLNLISVF PDDTKITVKA PEDIAHDIVE WGQFHAGVSS GLRISKKATG ITGSWIAFNK PK ELDAYHG GFLLGLGLNG HLKNLEEWHI YNYLSPRNTH ISIGLLLGMS SSMKGSMDSK LIKVISVHLV AFLPSGSSDL NID LKLQTA GIIGMGMLYL NSRHKRMSDS IFAQLVSLLN VNDEMVADEE YRLAAGISLG LINLGAGQTK LRKWDSSLLG LGDD LPEDV YDSSDVEQNV MYEDLTTKLL EIVTSTYDVE NDWIPENSQI GAVIAIMFLF LKSNNFGISN MLKVDLKEIL KANIN TRPE LLMYREWASN MILWEFIGDD LSFIMKDVDI GVKFSELNTD LLPIYYTMAG RILAMGIRFA STGNLKIRNI LLSLVD KFL PLYQYPGKQN LDFRLTISVI NVLTNVIVVS LSMVMCASGD LEVLRRVKYL HEVASGPYSD LFQEIPSSKS DVSGVTQ VT SNTNTPGNSD RERVDETAAS LDDERSSNGS DISDPTAYLE DKKDIDDHYG KFISTNLALG FLFLGSGQYA LNTSTLES I AFLSMSVLPT YTTPHPLQEL KHFWSMAVEP RCLVIKDIST GDAVNNVPIE LVVEEDVEKE EVIREISTPC LLPDFSKIK SIRVKMHGYF PLEVNFTKDY SASDFFSGGT IIYIQRKSES VFENKASFRN VEDIHVALKR KAAESKNYSR LNLKNEQGNT TSSQLVESL GIQDLTMVEL DTLLSAGNNT ALTDSESYNL GLLCSDKNSG DILDCQLELW YKSFGPHDE

UniProtKB: Anaphase-promoting complex subunit 1

+
Macromolecule #8: Anaphase-promoting complex subunit 5

MacromoleculeName: Anaphase-promoting complex subunit 5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 79.355641 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSKYGPLGIT NFITPYDLCI LILIHAHCSQ DNGISVPTAV FLRLISPTRP SLEWNPLLKD NSNLRSSSIV PPPVLPILDN IIRILLDDK DGNKIALTLM GYLEAINGLD SINRLMMDLE KNCLVNNYRS MKMRTTSTRR QMTRASFLGT FLSTCIRKYQ I GDFEMRET ...String:
MSKYGPLGIT NFITPYDLCI LILIHAHCSQ DNGISVPTAV FLRLISPTRP SLEWNPLLKD NSNLRSSSIV PPPVLPILDN IIRILLDDK DGNKIALTLM GYLEAINGLD SINRLMMDLE KNCLVNNYRS MKMRTTSTRR QMTRASFLGT FLSTCIRKYQ I GDFEMRET IWINLQNFKT VFKHTPLWLR FKDNVHIQKV KNCLLANDEI SVEDQQMVEF FQHFNNGNDA DSKTMNEENY GT LISIQHL QSIVNRQIVN WLDNTEFNLM GQEETSSTYE EQSGLVFDLL DTLSLNDATK FPLIFILKYL EAIKENSYQT ALD SLHNYF DYKSTGNSQN YFHISLLSLA TFHSSFNECD AAINSFEEAT RIARENKDME TLNLIMIWII NFIEVHPEYA NRFY ITVEQ IIKYLKNSSD VEDANIFSNA YKFETLLSMV KESKTAEVSS SLLKFMAITL QNVPSQNFDL FQSLVSYEVK FWKEL GYES ISDVYEKFLS KTSSSSLRNY DSSIINQDIK VAFKALEEDD FLKVKQYLLK SESLELDYDQ KINLKYLRVK YLVKIG DYD LSMRLINQYV KECCEEVADS NWRFKFEIES INVLLLSDVG IRSLPKIIKL IDEYKEIGNP LRCVILLLKL CEVLIQV GK SMEAECLISC NLSTILEFPF VRKKTDELLE SLSVEEDRDV QMT

UniProtKB: Anaphase-promoting complex subunit 5

+
Macromolecule #9: Anaphase-promoting complex subunit CDC23

MacromoleculeName: Anaphase-promoting complex subunit CDC23 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 73.197984 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNDDSQDKII HDIRIQLRKA ATELSRWKLY GSSKWAAEAL AGLAEAIDVD QTHSLADESP LRNKQGVPKQ MFEIPQNGFG LSETEYDLY LLGSTLFDAK EFDRCVFFLK DVTNPYLKFL KLYSKFLSWD KKSQESMENI LTTGKFTDEM YRANKDGDGS G NEDINQSG ...String:
MNDDSQDKII HDIRIQLRKA ATELSRWKLY GSSKWAAEAL AGLAEAIDVD QTHSLADESP LRNKQGVPKQ MFEIPQNGFG LSETEYDLY LLGSTLFDAK EFDRCVFFLK DVTNPYLKFL KLYSKFLSWD KKSQESMENI LTTGKFTDEM YRANKDGDGS G NEDINQSG HQRANLKMVS NEHESQSNIS SILKEINTFL ESYEIKIDDD EADLGLALLY YLRGVILKQE KNISKAMSSF LK SLSCYSF NWSCWLELMD CLQKVDDALL LNNYLYQNFQ FKFSENLGSQ RTIEFNIMIK FFKLKVFEEL NGQLEDYFED LEF LLQVFP NFTFLKAYNA TISYNNLDYV TAESRFDDIV KQDPYRLNDL ETYSNILYVM QKNSKLAYLA QFVSQIDRFR PETC CIIAN YYSARQEHEK SIMYFRRALT LDKKTTNAWT LMGHEFVELS NSHAAIECYR RAVDICPRDF KAWFGLGQAY ALLDM HLYS LYYFQKACTL KPWDRRIWQV LGECYSKTGN KVEAIKCYKR SIKASQTVDQ NTSIYYRLAQ LYEELEDLQE CKKFMM KCV DVEELLEGIV TDETVKARLW LAIFEIKAGN YQLAYDYAMG VSSGTSQEIE EARMLARECR RHM

UniProtKB: Anaphase-promoting complex subunit CDC23

+
Macromolecule #10: Anaphase-promoting complex subunit SWM1

MacromoleculeName: Anaphase-promoting complex subunit SWM1 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 19.37791 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSSSSYRDSY FQYRHLPAPH HILYAEWNQD ILALPDEVAN ITMAMKDNTR TDAEEGRAPQ DGERNSNVRE SAQGKALMTS EQNSNRYWN SFHDEDDWNL FNGMELESNG VVTFAGQAFD HSLNGGTNSR NDGANEPRKE TITGSIFDRR ITQLAYARNN G WHELALPQ SR

UniProtKB: Anaphase-promoting complex subunit SWM1

+
Macromolecule #11: Anaphase-promoting complex subunit MND2

MacromoleculeName: Anaphase-promoting complex subunit MND2 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 42.881523 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MARALRDISL FNDIRKDQNS AGAKHERYNM RDLRSKKNQH VNGIDDYEDD SLDRFIRRKK SRVVKYIPSL SAYNVFNEFP YYPTSASQL LDGKLDEFLM LSEQYKSRLP KIRKLGWNRF KPIGINKTMY ELEMLRSRAR AQNAEGNNEE DFRQHDSREE D PRNNGSIG ...String:
MARALRDISL FNDIRKDQNS AGAKHERYNM RDLRSKKNQH VNGIDDYEDD SLDRFIRRKK SRVVKYIPSL SAYNVFNEFP YYPTSASQL LDGKLDEFLM LSEQYKSRLP KIRKLGWNRF KPIGINKTMY ELEMLRSRAR AQNAEGNNEE DFRQHDSREE D PRNNGSIG RVILPHILQE NEEYDTGEGV TGLHSMPNDS MAILANNSAN NSQNEEVSEE DEISYDYDAE FDHVVDEDDN EE GEVPGEG VEGIEVQRER IVPDDLLMRP TSLSRSLQQF VEEAHHLDRN PYDIDSDNDG EDSKVELDMN PDFEDDVGRE HDY NSEYSQ EPTSYGGITP DLASNWRNWT RERITSLDEL MERRARQQRG QD

UniProtKB: Anaphase-promoting complex subunit MND2

+
Macromolecule #12: Anaphase-promoting complex subunit 4

MacromoleculeName: Anaphase-promoting complex subunit 4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 75.345688 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSSPINDYFI DYNPLFPIFA TRIAKGLAIY RVSDHARLAV IPIRNINLVA NYDWDTTTGK FLSIFFKDGT IRIHDIFKDG RLVSFLRIP STKISKGIWD RIPLRYEPNN RDFACNIIDD LPKLIRFVKD SKRINIVPYT QPNSLWRGPD EDDLDSNEKL D VHVVFNEG ...String:
MSSPINDYFI DYNPLFPIFA TRIAKGLAIY RVSDHARLAV IPIRNINLVA NYDWDTTTGK FLSIFFKDGT IRIHDIFKDG RLVSFLRIP STKISKGIWD RIPLRYEPNN RDFACNIIDD LPKLIRFVKD SKRINIVPYT QPNSLWRGPD EDDLDSNEKL D VHVVFNEG NDKITVFFNG DYAVFLSVDN IENENSLKSI IKVQDGFYQC FYEDGTVQTL NLGPLLQSKS SVNLLNYIMV IK ELIGYML THLEFINREL ATPYLDFVKR LCDEAYGYGK LKSELEALFL LGEISCDLED WLCNSVGEKN FKRWKYLGCE AYQ KTVQIL TLIFVPACER IIIYVEKLRA ILQAFSIQNK LSYTSDLTAV EVLLKSSQKL LTMTLNSIIG LGRDETLFEK FFIW FNDRL HEALDEDYKL KFQFEDDLYF GYDLLSYFDR ILSKKGTEPS SIIDVKLYRD LINSMSDMEK DIAQSNVNSH IQQHI LVDL KTDVFAQKYP SSQINLLDAI KLPKHNYIVY LIQVTKHNSA QEPFSEENKK KLYIGTLKDE NLGIISKESS VKIPAL FKS YRLSSTRFVP NRVHSLLRDI GLSDSNYHSS HVTDYRGENY ENEEDDGTIA IPAYIRENRE NDDFIACTAK VSVDGRS AS LVFPKEKQNV

UniProtKB: Anaphase-promoting complex subunit 4

+
Macromolecule #13: Anaphase-promoting complex subunit DOC1

MacromoleculeName: Anaphase-promoting complex subunit DOC1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 28.810664 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDPIGINKVL DHLAPSELIK PVKSCHNKPS VLVLDDRIVD AATKDLYVNG FQEEIQYQNP TPENLQHMFH QGIEILDSAR MINVTHLAL WKPSSFKLGN PVDFALDDNY DTFWQSDGGQ PHQLDIMFSK RMDICVMAIF FSMIADESYA PSLVKVYAGH S PSDARFYK ...String:
MDPIGINKVL DHLAPSELIK PVKSCHNKPS VLVLDDRIVD AATKDLYVNG FQEEIQYQNP TPENLQHMFH QGIEILDSAR MINVTHLAL WKPSSFKLGN PVDFALDDNY DTFWQSDGGQ PHQLDIMFSK RMDICVMAIF FSMIADESYA PSLVKVYAGH S PSDARFYK MLEVRNVNGW VALRFLDNRE DDQLLKCQFI RLLFPVNHEN GKDTHLRGIR LYVPSNEPHQ DTHEWAQTLP ET NNVFQDA ILR

UniProtKB: Anaphase-promoting complex subunit DOC1

+
Macromolecule #14: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 14 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8.3
Component:
ConcentrationFormulaName
50.0 mMTris.HClTris
250.0 mMNaClSodium chloridesodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 4 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 75 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 51.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 9.0 µm / Nominal defocus min: 2.6 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 1 pixel / Digitization - Dimensions - Height: 1 pixel / Number grids imaged: 1 / Number real images: 4362 / Average exposure time: 2.0 sec. / Average electron dose: 59.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 815009
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 10 / Avg.num./class: 50000 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionNumber classes used: 10 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 372535

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8a5y:
S. cerevisiae apo unphosphorylated APC/C.

+
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