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- PDB-4ui9: Atomic structure of the human Anaphase-Promoting Complex -

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Basic information

Entry
Database: PDB / ID: 4ui9
TitleAtomic structure of the human Anaphase-Promoting Complex
Components
  • (ANAPHASE-PROMOTING COMPLEX SUBUNIT ...) x 12
  • (CELL DIVISION CYCLE PROTEIN ...) x 4
  • (PEPTIDE) x 2
  • F-BOX ONLY PROTEIN 5
  • FIZZY-RELATED PROTEIN HOMOLOG
KeywordsCELL CYCLE / UBIQUITINATION / APC/C / APC SUBUNITS / ANAPHASE PROMOTING COMPLEX
Function / homology
Function and homology information


negative regulation of DNA endoreduplication / negative regulation of mitotic metaphase/anaphase transition / negative regulation of meiotic nuclear division / positive regulation of biomineral tissue development / 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 / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint ...negative regulation of DNA endoreduplication / negative regulation of mitotic metaphase/anaphase transition / negative regulation of meiotic nuclear division / positive regulation of biomineral tissue development / 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 / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of synapse maturation / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / vesicle organization / Phosphorylation of Emi1 / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / lens fiber cell differentiation / positive regulation of synaptic plasticity / regulation of exit from mitosis / Phosphorylation of the APC/C / anaphase-promoting complex binding / negative regulation of ubiquitin-protein transferase activity / ubiquitin ligase activator activity / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / spindle assembly involved in female meiosis I / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / regulation of mitotic metaphase/anaphase transition / meiotic spindle / positive regulation of dendrite morphogenesis / oocyte maturation / ubiquitin-ubiquitin ligase activity / negative regulation of ubiquitin protein ligase activity / regulation of mitotic nuclear division / mitotic metaphase chromosome alignment / molecular function inhibitor activity / G1/S-Specific Transcription / regulation of DNA replication / microtubule polymerization / mitotic G2 DNA damage checkpoint signaling / negative regulation of cellular senescence / Regulation of APC/C activators between G1/S and early anaphase / cullin family protein binding / ubiquitin ligase inhibitor activity / ubiquitin-like ligase-substrate adaptor activity / Transcriptional Regulation by VENTX / positive regulation of axon extension / heterochromatin / positive regulation of osteoblast differentiation / Cyclin A:Cdk2-associated events at S phase entry / regulation of mitotic cell cycle / 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 / 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 / CDK-mediated phosphorylation and removal of Cdc6 / mitotic spindle / kinetochore / spindle / Separation of Sister Chromatids / ubiquitin-protein transferase activity / microtubule cytoskeleton / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / mitotic cell cycle / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / nuclear membrane / protein phosphatase binding / molecular adaptor activity / cell differentiation / protein ubiquitination / cell cycle / cell division / negative regulation of gene expression / DNA repair / centrosome / ubiquitin protein ligase binding / DNA damage response / positive regulation of cell population proliferation / nucleolus / protein kinase binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / : / F-box domain / Anaphase-promoting complex subunit 15 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 4, metazoa / : ...Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / : / F-box domain / Anaphase-promoting complex subunit 15 / The WD repeat Cdc20/Fizzy family / Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 4, metazoa / : / Anaphase-promoting complex subunit 5, N-terminal domain / 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 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 / 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 / F-box domain / Tetratricopeptide repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Galactose-binding domain-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / TPR repeat region circular profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / 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. / WD domain, G-beta repeat / WD40 repeats / Jelly Rolls / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChang, L. / Zhang, Z. / Yang, J. / McLaughlin, S.H. / Barford, D.
CitationJournal: Nature / Year: 2015
Title: Atomic structure of the APC/C and its mechanism of protein ubiquitination.
Authors: Leifu Chang / Ziguo Zhang / Jing Yang / Stephen H McLaughlin / David Barford /
Abstract: The anaphase-promoting complex (APC/C) is a multimeric RING E3 ubiquitin ligase that controls chromosome segregation and mitotic exit. Its regulation by coactivator subunits, phosphorylation, the ...The anaphase-promoting complex (APC/C) is a multimeric RING E3 ubiquitin ligase that controls chromosome segregation and mitotic exit. Its regulation by coactivator subunits, phosphorylation, the mitotic checkpoint complex and interphase early mitotic inhibitor 1 (Emi1) ensures the correct order and timing of distinct cell-cycle transitions. Here we use cryo-electron microscopy to determine atomic structures of APC/C-coactivator complexes with either Emi1 or a UbcH10-ubiquitin conjugate. These structures define the architecture of all APC/C subunits, the position of the catalytic module and explain how Emi1 mediates inhibition of the two E2s UbcH10 and Ube2S. Definition of Cdh1 interactions with the APC/C indicates how they are antagonized by Cdh1 phosphorylation. The structure of the APC/C with UbcH10-ubiquitin reveals insights into the initiating ubiquitination reaction. Our results provide a quantitative framework for the design of future experiments to investigate APC/C functions in vivo.
History
DepositionMar 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Other
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.4Apr 24, 2019Group: Data collection / Other / Category: atom_sites / Item: _atom_sites.fract_transf_matrix[1][1]
Revision 1.5May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Assembly

Deposited unit
A: ANAPHASE-PROMOTING COMPLEX SUBUNIT 1
B: ANAPHASE-PROMOTING COMPLEX SUBUNIT 11
C: CELL DIVISION CYCLE PROTEIN 23 HOMOLOG
D: ANAPHASE-PROMOTING COMPLEX SUBUNIT 15
E: ANAPHASE-PROMOTING COMPLEX SUBUNIT 16
F: CELL DIVISION CYCLE PROTEIN 27 HOMOLOG
G: ANAPHASE-PROMOTING COMPLEX SUBUNIT CDC26
H: CELL DIVISION CYCLE PROTEIN 27 HOMOLOG
I: ANAPHASE-PROMOTING COMPLEX SUBUNIT 4
J: CELL DIVISION CYCLE PROTEIN 16 HOMOLOG
K: CELL DIVISION CYCLE PROTEIN 16 HOMOLOG
L: ANAPHASE-PROMOTING COMPLEX SUBUNIT 10
M: ANAPHASE-PROMOTING COMPLEX SUBUNIT 13
N: ANAPHASE-PROMOTING COMPLEX SUBUNIT 2
O: ANAPHASE-PROMOTING COMPLEX SUBUNIT 5
P: CELL DIVISION CYCLE PROTEIN 23 HOMOLOG
R: FIZZY-RELATED PROTEIN HOMOLOG
S: F-BOX ONLY PROTEIN 5
T: PEPTIDE
U: PEPTIDE
W: ANAPHASE-PROMOTING COMPLEX SUBUNIT CDC26
X: ANAPHASE-PROMOTING COMPLEX SUBUNIT 7
Y: ANAPHASE-PROMOTING COMPLEX SUBUNIT 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,272,96128
Polymers1,272,63423
Non-polymers3275
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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ANAPHASE-PROMOTING COMPLEX SUBUNIT ... , 12 types, 13 molecules ABDEGILMNOWXY

#1: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 1 / APC1 / CYCLOSOME SUBUNIT 1 / MITOTIC CHECKPOINT REGULATOR / TESTIS-SPECIFIC GENE 24 PROTEIN / APC1 ...APC1 / CYCLOSOME SUBUNIT 1 / MITOTIC CHECKPOINT REGULATOR / TESTIS-SPECIFIC GENE 24 PROTEIN / APC1 / CYCLOSOME SUBUNIT 1 / MITOTIC CHECKPOINT REGULATOR / TESTIS-SPECIFIC GENE 24 PROTEIN


Mass: 216777.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9H1A4
#2: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 11 / APC11 / CYCLOSOME SUBUNIT 11 / HEPATOCELLULAR CARCINOMA-ASSOCIATED RING FINGER PROTEIN / APC11 / ...APC11 / CYCLOSOME SUBUNIT 11 / HEPATOCELLULAR CARCINOMA-ASSOCIATED RING FINGER PROTEIN / APC11 / CYCLOSOME SUBUNIT 11 / HEPATOCELLULAR CARCINOMA- ASSOCIATED RING FINGER PROTEIN


Mass: 9866.702 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9NYG5
#4: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 15 / APC15 / APC15


Mass: 14302.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P60006
#5: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 16 / APC16 / CYCLOSOME SUBUNIT 16 / APC16 / CYCLOSOME SUBUNIT 16


Mass: 11677.995 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q96DE5
#7: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT CDC26 / ANAPHASE-PROMOTING COMPLEX SUBUNIT 12 / APC12 / CELL DIVISION CYCLE PROTEIN 26 HOMOLOG / ANAPHASE- ...ANAPHASE-PROMOTING COMPLEX SUBUNIT 12 / APC12 / CELL DIVISION CYCLE PROTEIN 26 HOMOLOG / ANAPHASE-PROMOTING COMPLEX SUBUNIT 12 / APC12 / CELL DIVISION CYCLE PROTEIN 26 HOMOLOG


Mass: 9808.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q8NHZ8
#8: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 4 / APC4 / CYCLOSOME SUBUNIT 4 / APC4 / CYCLOSOME SUBUNIT 4


Mass: 92205.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9UJX5
#11: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 10 / APC10 / CYCLOSOME SUBUNIT 10 / APC10 / CYCLOSOME SUBUNIT 10


Mass: 21021.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9UM13
#12: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 13 / APC13 / CYCLOSOME SUBUNIT 13 / APC13 / CYCLOSOME SUBUNIT 13


Mass: 8528.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9BS18
#13: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 2 / APC2 / CYCLOSOME SUBUNIT 2 / APC2 / CYCLOSOME SUBUNIT 2


Mass: 93938.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9UJX6
#14: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 5 / APC5 / CYCLOSOME SUBUNIT 5 / APC5 / CYCLOSOME SUBUNIT 5


Mass: 85216.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9UJX4
#19: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT CDC26 / ANAPHASE-PROMOTING COMPLEX SUBUNIT 12 / APC12 / CELL DIVISION CYCLE PROTEIN 26 HOMOLOG / ANAPHASE- ...ANAPHASE-PROMOTING COMPLEX SUBUNIT 12 / APC12 / CELL DIVISION CYCLE PROTEIN 26 HOMOLOG / ANAPHASE-PROMOTING COMPLEX SUBUNIT 12 / APC12 / CELL DIVISION CYCLE PROTEIN 26 HOMOLOG


Mass: 9793.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q8NHZ8
#20: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 7 / APC7 / CYCLOSOME SUBUNIT 7 / APC7 / CYCLOSOME SUBUNIT 7


Mass: 63106.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9UJX3

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CELL DIVISION CYCLE PROTEIN ... , 4 types, 6 molecules CPFHJK

#3: Protein CELL DIVISION CYCLE PROTEIN 23 HOMOLOG / ANAPHASE-PROMOTING COMPLEX SUBUNIT 8 / APC8 / CYCLOSOME SUBUNIT 8 / ANAPHASE-PROMOTING COMPLEX ...ANAPHASE-PROMOTING COMPLEX SUBUNIT 8 / APC8 / CYCLOSOME SUBUNIT 8 / ANAPHASE-PROMOTING COMPLEX SUBUNIT 8 / APC8 / CYCLOSOME SUBUNIT 8


Mass: 68356.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9UJX2
#6: Protein CELL DIVISION CYCLE PROTEIN 27 HOMOLOG / ANAPHASE-PROMOTING COMPLEX SUBUNIT 3 / APC3 / CDC27 HOMOLOG / CDC27HS / H-NUC / ANAPHASE-PROMOTING ...ANAPHASE-PROMOTING COMPLEX SUBUNIT 3 / APC3 / CDC27 HOMOLOG / CDC27HS / H-NUC / ANAPHASE-PROMOTING COMPLEX SUBUNIT 3 / APC3 / CDC27 HOMOLOG / CDC27HS / H-NUC


Mass: 92005.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P30260
#9: Protein CELL DIVISION CYCLE PROTEIN 16 HOMOLOG / ANAPHASE-PROMOTING COMPLEX SUBUNIT 6 / APC6 / CDC16 HOMOLOG / CDC16HS / CYCLOSOME SUBUNIT 6 / ...ANAPHASE-PROMOTING COMPLEX SUBUNIT 6 / APC6 / CDC16 HOMOLOG / CDC16HS / CYCLOSOME SUBUNIT 6 / ANAPHASE-PROMOTING COMPLEX SUBUNIT 6 / APC6 / CDC16 HOMOLOG / CDC16HS / CYCLOSOME SUBUNIT 6


Mass: 71747.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q13042
#10: Protein CELL DIVISION CYCLE PROTEIN 16 HOMOLOG / ANAPHASE-PROMOTING COMPLEX SUBUNIT 6 / APC6 / CDC16 HOMOLOG / CDC16HS / CYCLOSOME SUBUNIT 6 / ...ANAPHASE-PROMOTING COMPLEX SUBUNIT 6 / APC6 / CDC16 HOMOLOG / CDC16HS / CYCLOSOME SUBUNIT 6 / ANAPHASE-PROMOTING COMPLEX SUBUNIT 6 / APC6 / CDC16 HOMOLOG / CDC16HS / CYCLOSOME SUBUNIT 6


Mass: 71806.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q13042

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Protein , 2 types, 2 molecules RS

#15: Protein FIZZY-RELATED PROTEIN HOMOLOG / FZR / CDC20-LIKE PROTEIN 1 / CDH1/HCT1 HOMOLOG / HCDH1 / FZR / C DC20-LIKE PROTEIN 1 / CDH1/HCT1 ...FZR / CDC20-LIKE PROTEIN 1 / CDH1/HCT1 HOMOLOG / HCDH1 / FZR / C DC20-LIKE PROTEIN 1 / CDH1/HCT1 HOMOLOG / HCDH1


Mass: 54838.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9UM11
#16: Protein F-BOX ONLY PROTEIN 5 / EARLY MITOTIC INHIBITOR 1 / EARLY MITOTIC INHIBITOR 1


Mass: 50297.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9UKT4

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Protein/peptide , 2 types, 2 molecules TU

#17: Protein/peptide PEPTIDE


Mass: 1609.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human)
#18: Protein/peptide PEPTIDE


Mass: 2258.669 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q9UKT4*PLUS

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Non-polymers , 1 types, 5 molecules

#21: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: HUMAN ANAPHASE-PROMOTING COMPLEX / Type: COMPLEX
Buffer solutionpH: 8
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Feb 9, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 78000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1REFMACmodel fitting
2RELION3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Num. of particles: 202084 / Nominal pixel size: 1.36 Å / Actual pixel size: 1.36 Å / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Refinement stepCycle: LAST / Highest resolution: 3.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms66443 0 5 0 66448

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