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- PDB-5a31: Structure of the human APC-Cdh1-Hsl1-UbcH10 complex. -

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Entry
Database: PDB / ID: 5a31
TitleStructure of the human APC-Cdh1-Hsl1-UbcH10 complex.
Components
  • (ANAPHASE-PROMOTING COMPLEX SUBUNIT ...) x 14
  • (THE ANAPHASE-PROMOTING COMPLEX CHAIN ...) x 4
  • CELL DIVISION CYCLE PROTEIN 23 HOMOLOG
  • FUSION PROTEIN - UBIQUITIN-CONJUGATING ENZYME E2 C, UBIQUITIN-CONJUGATING ENZYME E2 S
KeywordsCELL CYCLE / UBIQUITINATION / APC/C
Function / homology
Function and homology information


negative regulation of mitotic spindle pole body separation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring contraction / deactivation of mitotic spindle assembly checkpoint / positive regulation of anaphase-promoting complex-dependent catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of exit from mitosis / free ubiquitin chain polymerization / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase ...negative regulation of mitotic spindle pole body separation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring contraction / deactivation of mitotic spindle assembly checkpoint / positive regulation of anaphase-promoting complex-dependent catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of exit from mitosis / free ubiquitin chain polymerization / 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 / anaphase-promoting complex / protein branched polyubiquitination / Aberrant regulation of mitotic exit in cancer due to RB1 defects / metaphase/anaphase transition of mitotic cell cycle / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / positive regulation of synaptic plasticity / regulation of exit from mitosis / Phosphorylation of the APC/C / anaphase-promoting complex binding / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / positive regulation of ubiquitin-dependent protein catabolic process / ubiquitin ligase activator activity / positive regulation of ubiquitin protein ligase activity / protein K11-linked ubiquitination / enzyme-substrate adaptor activity / regulation of mitotic metaphase/anaphase transition / exit from mitosis / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / mitotic metaphase chromosome alignment / ubiquitin conjugating enzyme activity / Antigen processing: Ubiquitination & Proteasome degradation / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin-like protein ligase binding / cullin family protein binding / Transcriptional Regulation by VENTX / ubiquitin ligase complex / positive regulation of axon extension / heterochromatin / protein K48-linked ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / cyclin binding / nuclear periphery / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of mitotic cell cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / 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 / mitotic spindle / spindle / protein polyubiquitination / Separation of Sister Chromatids / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / 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 / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein ubiquitination / cell division / negative regulation of gene expression / centrosome / ubiquitin protein ligase binding / nucleolus / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Anaphase-promoting complex subunit 15 / Anaphase-promoting complex subunit 15 / The WD repeat Cdc20/Fizzy family / 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 subunit 15 / Anaphase-promoting complex subunit 15 / The WD repeat Cdc20/Fizzy family / 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 / 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 / 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 / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Tetratricopeptide repeat / Ubiquitin-conjugating enzyme/RWD-like / 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. / 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
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 C / Cell division cycle protein 27 homolog / APC/C activator protein CDH1 / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit CDC26 / Anaphase-promoting complex subunit 16 / Anaphase-promoting complex subunit 13 / Anaphase-promoting complex subunit 1 ...Ubiquitin-conjugating enzyme E2 C / Cell division cycle protein 27 homolog / APC/C activator protein CDH1 / Anaphase-promoting complex subunit 15 / Cell division cycle protein 16 homolog / Anaphase-promoting complex subunit 13 / 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 / Anaphase-promoting complex subunit 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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
DepositionMay 26, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.2Oct 16, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 18, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_prop / struct_site
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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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: ANAPHASE-PROMOTING COMPLEX SUBUNIT 3
G: ANAPHASE-PROMOTING COMPLEX SUBUNIT CDC26
H: ANAPHASE-PROMOTING COMPLEX SUBUNIT 3
I: ANAPHASE-PROMOTING COMPLEX SUBUNIT 4
J: ANAPHASE-PROMOTING COMPLEX SUBUNIT 6
K: ANAPHASE-PROMOTING COMPLEX SUBUNIT 6
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
Q: FUSION PROTEIN - UBIQUITIN-CONJUGATING ENZYME E2 C, UBIQUITIN-CONJUGATING ENZYME E2 S
R: THE ANAPHASE-PROMOTING COMPLEX CHAIN R
T: THE ANAPHASE-PROMOTING COMPLEX CHAIN T
U: THE ANAPHASE-PROMOTING COMPLEX CHAIN U
V: THE ANAPHASE-PROMOTING COMPLEX CHAIN V
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)1,166,48727
Polymers1,166,29124
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ANAPHASE-PROMOTING COMPLEX SUBUNIT ... , 14 types, 17 molecules ABDEFHGWIJKLMNOXY

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


Mass: 159616.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9H1A4*PLUS
#2: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 11 / APC11 / CYCLOSOME SUBUNIT 11 / HEPATOCELLULAR CARCINOMA-ASSOC IATED RING FINGER PROTEIN


Mass: 9866.702 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9NYG5
#4: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 15 / APC15


Mass: 14302.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P60006
#5: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 16 / APC16 / CYCLOSOME SUBUNIT 16


Mass: 11677.995 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q96DE5
#6: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 3 / CELL DIVISION CYCLE PROTEIN 27 HOMOLOG / APC3 / CDC27 HOMOLOG / CDC27HS / H-NUC


Mass: 92005.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P30260
#7: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT CDC26 / ANAPHASE-PROMOTING COMPLEX SUBUNIT 12 / APC12 / CELL DIVISION CYCLE PROTEIN 26 HOMOLOG


Mass: 9793.999 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q8NHZ8
#8: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 4 / APC4 / CYCLOSOME SUBUNIT 4


Mass: 92205.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9UJX5
#9: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 6 / CELL DIVISION CYCLE PROTEIN 16 HOMOLOG / APC6 / CDC16 HOMOLOG / CDC16HS / CYCLOSOME SUBUNIT 6


Mass: 71631.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q13042
#10: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 6 / CELL DIVISION CYCLE PROTEIN 16 HOMOLOG / APC6 / CDC16 HOMOLOG / CDC16HS / CYCLOSOME SUBUNIT 6


Mass: 71806.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q13042
#11: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 10 / APC10 / CYCLOSOME SUBUNIT 10


Mass: 21282.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9UM13
#12: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 13 / APC13 / CYCLOSOME SUBUNIT 13


Mass: 8528.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q2NKV2, UniProt: Q9BS18*PLUS
#13: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 2 / APC2 / CYCLOSOME SUBUNIT 2


Mass: 79116.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9UJX6*PLUS
#14: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 5 / APC5 / CYCLOSOME SUBUNIT 5


Mass: 85087.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9UJX4
#20: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 7 / APC7 / CYCLOSOME SUBUNIT 7 / THE ANAPHASE-PROMOTING COMPLEX


Mass: 66832.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9UJX3

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Protein , 2 types, 3 molecules CPQ

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


Mass: 68905.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9UJX2
#15: Protein FUSION PROTEIN - UBIQUITIN-CONJUGATING ENZYME E2 C, UBIQUITIN-CONJUGATING ENZYME E2 S / (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME C / E2 UBIQUITIN-CONJUGATING ENZYME C / UBCH10 / ...(E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME C / E2 UBIQUITIN-CONJUGATING ENZYME C / UBCH10 / UBIQUITIN CARRIER PROTEIN C / UBIQUITIN-PROTEIN LIGASE C / UBIQUITIN CARRIER PROTEIN S / E2 UBIQUITIN-CONJUGATING ENZYME S / UBIQUITIN-CONJUGATING ENZYME E2-24 KDA / E2-EPF / UBIQUITIN-CONJUGATING ENZYME E2-EPF5 / UBIQUITIN-PROTEIN LIGASE S


Mass: 17793.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: O00762*PLUS, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme, E2 ubiquitin-conjugating enzyme

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THE ANAPHASE-PROMOTING COMPLEX CHAIN ... , 4 types, 4 molecules RTUV

#16: Protein THE ANAPHASE-PROMOTING COMPLEX CHAIN R


Mass: 42944.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P53197*PLUS
#17: Protein/peptide THE ANAPHASE-PROMOTING COMPLEX CHAIN T


Mass: 1876.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper)
#18: Protein/peptide THE ANAPHASE-PROMOTING COMPLEX CHAIN U


Mass: 2060.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper)
#19: Protein/peptide THE ANAPHASE-PROMOTING COMPLEX CHAIN V


Mass: 1421.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: TRICHOPLUSIA NI (cabbage looper)

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Non-polymers , 1 types, 3 molecules

#21: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Sequence detailsTHE CHAINS A AND N CORRESPOND TO UNIPROT Q9H1A4 AND Q9UJX6 RESPECTIVELY. CHAIN Q RESIDUES 1-179 AND ...THE CHAINS A AND N CORRESPOND TO UNIPROT Q9H1A4 AND Q9UJX6 RESPECTIVELY. CHAIN Q RESIDUES 1-179 AND RESIDUES 183-329 CAN BE MAPPED TO UNIPROT O00762 AND Q16763 RESPECTIVELY. THE RESIDUES 180-182 IN CHAIN Q SERVE AS A LINKER BETWEEN THE SAMPLE SEQUENCE FOR UNP O00762 AND UNP Q16763. THERE ARE STRETCHES OF UNK RESIDUES BUILT INTO THESE CHAINS BECUASE THE REGISTER OF THESE AMINO ACIDS TO THE SEQUENCE REMAINS UNKNOWN. THE SAME IS TRUE CHAINS T AND U

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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: Jul 12, 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: 16 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
1REFMACmodel fitting
2RELION3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Num. of particles: 19939 / Nominal pixel size: 1.36 Å / Actual pixel size: 1.36 Å / Symmetry type: POINT
RefinementHighest resolution: 4.3 Å
Refinement stepCycle: LAST / Highest resolution: 4.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms67667 0 3 0 67670

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