[English] 日本語
Yorodumi
- PDB-4ui9: Atomic structure of the human Anaphase-Promoting Complex -

+
Open data


ID or keywords:

Loading...

-
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 / positive regulation of biomineral tissue development / negative regulation of meiotic nuclear division / positive regulation of anaphase-promoting complex-dependent catabolic process / negative regulation of mitotic metaphase/anaphase transition / positive regulation of mesenchymal stem cell migration / regulation of meiotic nuclear division / Mitotic Metaphase/Anaphase Transition / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase ...negative regulation of DNA endoreduplication / positive regulation of biomineral tissue development / negative regulation of meiotic nuclear division / positive regulation of anaphase-promoting complex-dependent catabolic process / negative regulation of mitotic metaphase/anaphase transition / positive regulation of mesenchymal stem cell migration / regulation of meiotic nuclear division / Mitotic Metaphase/Anaphase Transition / 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 / protein branched polyubiquitination / 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 / anaphase-promoting complex-dependent catabolic process / metaphase/anaphase transition of mitotic cell cycle / lens fiber cell differentiation / positive regulation of synaptic plasticity / regulation of exit from mitosis / anaphase-promoting complex binding / Phosphorylation of the APC/C / negative regulation of ubiquitin-protein transferase activity / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / spindle assembly involved in female meiosis I / protein K11-linked ubiquitination / meiotic spindle / enzyme-substrate adaptor activity / positive regulation of dendrite morphogenesis / regulation of mitotic metaphase/anaphase transition / 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 / mitotic G2 DNA damage checkpoint signaling / negative regulation of cellular senescence / microtubule polymerization / Regulation of APC/C activators between G1/S and early anaphase / cullin family protein binding / ubiquitin ligase inhibitor activity / Transcriptional Regulation by VENTX / ubiquitin-like ligase-substrate adaptor activity / positive regulation of axon extension / positive regulation of osteoblast differentiation / protein K48-linked ubiquitination / heterochromatin / 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 / brain development / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / CDK-mediated phosphorylation and removal of Cdc6 / mitotic spindle / kinetochore / spindle / ubiquitin-protein transferase activity / Separation of Sister Chromatids / microtubule cytoskeleton / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein phosphatase binding / nuclear membrane / molecular adaptor activity / cell differentiation / protein ubiquitination / cell division / negative regulation of gene expression / DNA repair / centrosome / DNA damage response / ubiquitin protein ligase binding / positive regulation of cell population proliferation / nucleolus / protein kinase binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding
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 / Anaphase-promoting complex subunit 1, C-terminal ...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 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 / 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 / Tetratricopeptide repeat domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Tetratricopeptide repeat / Herpes Virus-1 / Galactose-binding domain-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Zinc finger, RING-type / 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. / Jelly Rolls / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2924
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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