[English] 日本語
Yorodumi
- PDB-4yii: Structure of an APC2-UBCH10 complex reveals distinctive cullin-RI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yii
TitleStructure of an APC2-UBCH10 complex reveals distinctive cullin-RING ligase mechanism for Anaphase-promoting complex/Cyclosome
Components
  • Anaphase-promoting complex subunit 2
  • Ubiquitin-conjugating enzyme E2 C
Keywordsligase/cell cycle / ligase-cell cycle complex
Function / homology
Function and homology information


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 / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / 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 ...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 / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / 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 / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of synaptic plasticity / Phosphorylation of the APC/C / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / exit from mitosis / protein K11-linked ubiquitination / regulation of mitotic metaphase/anaphase transition / positive regulation of dendrite morphogenesis / E2 ubiquitin-conjugating enzyme / ubiquitin-like protein ligase binding / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin conjugating enzyme activity / Transcriptional Regulation by VENTX / positive regulation of axon extension / protein K48-linked ubiquitination / ubiquitin ligase complex / APC/C:Cdc20 mediated degradation of Cyclin B / regulation of mitotic cell cycle / APC-Cdc20 mediated degradation of Nek2A / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / 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 / CDK-mediated phosphorylation and removal of Cdc6 / protein polyubiquitination / Separation of Sister Chromatids / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / cell differentiation / protein ubiquitination / cell division / negative regulation of gene expression / ubiquitin protein ligase binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Anaphase-promoting complex subunit 2, C-terminal / Anaphase-promoting complex subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase promoting complex (APC) subunit 2 / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily ...Anaphase-promoting complex subunit 2, C-terminal / Anaphase-promoting complex subunit 2 / Anaphase promoting complex (APC) subunit 2 / Anaphase promoting complex (APC) subunit 2 / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 C / Anaphase-promoting complex subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsBrown, N.G. / Cho, S.E. / Schulman, B.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Crystal Structure of E2 Complex
Authors: Brown, N.G. / Cho, S.E. / Schulman, B.A.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
U: Ubiquitin-conjugating enzyme E2 C
A: Anaphase-promoting complex subunit 2


Theoretical massNumber of molelcules
Total (without water)27,6202
Polymers27,6202
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-14 kcal/mol
Surface area10900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.113, 33.188, 51.963
Angle α, β, γ (deg.)90.00, 100.12, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2 C / UbcH10 / Ubiquitin carrier protein C / Ubiquitin-protein ligase C


Mass: 17360.707 Da / Num. of mol.: 1 / Fragment: unp residues 27-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2C, UBCH10 / Production host: Escherichia coli (E. coli) / References: UniProt: O00762, ubiquitin-protein ligase
#2: Protein Anaphase-promoting complex subunit 2 / / APC2 / Cyclosome subunit 2


Mass: 10259.662 Da / Num. of mol.: 1 / Fragment: unp residues 735-822
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC2, APC2, KIAA1406 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UJX6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: PEG 3000, MES / PH range: 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2826 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 21055 / % possible obs: 94 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.4
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.347 / Num. unique all: 21055 / % possible all: 68.2

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LDD, 1I7K

1ldd

1i7k


Resolution: 1.804→44.272 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 967 4.91 %
Rwork0.1963 --
obs0.1985 19692 93.87 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.613 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8068 Å20 Å26.1647 Å2
2--11.4234 Å20 Å2
3----5.6166 Å2
Refinement stepCycle: LAST / Resolution: 1.804→44.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 0 64 1758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131747
X-RAY DIFFRACTIONf_angle_d1.4992383
X-RAY DIFFRACTIONf_dihedral_angle_d14.242626
X-RAY DIFFRACTIONf_chiral_restr0.107270
X-RAY DIFFRACTIONf_plane_restr0.007302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8042-1.89930.30451050.29972136X-RAY DIFFRACTION76
1.8993-2.01830.29251600.24322646X-RAY DIFFRACTION94
2.0183-2.17420.27781420.21132740X-RAY DIFFRACTION97
2.1742-2.3930.24761530.20282763X-RAY DIFFRACTION98
2.393-2.73920.26441300.19712808X-RAY DIFFRACTION98
2.7392-3.45090.25121410.19552772X-RAY DIFFRACTION97
3.4509-44.28530.21911360.18212860X-RAY DIFFRACTION97

+
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