[English] 日本語
Yorodumi
- PDB-2oxq: Structure of the UbcH5 :CHIP U-box complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oxq
TitleStructure of the UbcH5 :CHIP U-box complex
Components
  • STIP1 homology and U-Box containing protein 1
  • Ubiquitin-conjugating enzyme E2D 1
KeywordsLIGASE / protein-protein complex
Function / homology
Function and homology information


Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Regulation of APC/C activators between G1/S and early anaphase / APC/C:Cdc20 mediated degradation of mitotic proteins / APC-Cdc20 mediated degradation of Nek2A ...Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of Cyclin B / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Regulation of APC/C activators between G1/S and early anaphase / APC/C:Cdc20 mediated degradation of mitotic proteins / APC-Cdc20 mediated degradation of Nek2A / Senescence-Associated Secretory Phenotype (SASP) / Peroxisomal protein import / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of TNFR1 signaling / Antigen processing: Ubiquitination & Proteasome degradation / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Phosphorylation of the APC/C / Separation of Sister Chromatids / Ovarian tumor domain proteases / Neddylation / cerebellar Purkinje cell layer structural organization / regulation of glucocorticoid metabolic process / E2 ubiquitin-conjugating enzyme / TPR domain binding / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / Hsp70 protein binding / positive regulation of protein ubiquitination / Hsp90 protein binding / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA repair / signal transduction / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...CHIP, N-terminal tetratricopeptide repeat domain / CHIP/LubX , U box domain / CHIP N-terminal tetratricopeptide repeat domain / Anaphase-promoting complex, cyclosome, subunit 3 / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E2 ubiquitin-conjugating enzyme / E3 ubiquitin-protein ligase CHIP
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXu, Z. / Nix, J.C. / Devlin, K.I. / Misra, S.
CitationJournal: Bmc Struct.Biol. / Year: 2008
Title: Interactions between the quality control ubiquitin ligase CHIP and ubiquitin conjugating enzymes.
Authors: Xu, Z. / Kohli, E. / Devlin, K.I. / Bold, M. / Nix, J.C. / Misra, S.
History
DepositionFeb 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2D 1
B: Ubiquitin-conjugating enzyme E2D 1
C: STIP1 homology and U-Box containing protein 1
D: STIP1 homology and U-Box containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3387
Polymers52,2324
Non-polymers1063
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.042, 93.399, 144.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2D 1 / UBC4/5 homolog / yeast


Mass: 17057.529 Da / Num. of mol.: 2 / Fragment: UbcH5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ube2d1 / Plasmid: pHis-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2(DE3) / References: UniProt: Q6PC58, ubiquitin-protein ligase
#2: Protein STIP1 homology and U-Box containing protein 1


Mass: 9058.354 Da / Num. of mol.: 2 / Fragment: U-box domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: stub1 / Plasmid: pHis-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q7ZTZ6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.09 Å3/Da / Density % sol: 75.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.65M Ammonium Sulfate, 0.09M Bistris, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.24 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 7, 2006
Details: Rosenbaum-Rock monochromator 1: high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2: double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.9→55 Å / Num. all: 24307 / Num. obs: 24283 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 3.4 % / Biso Wilson estimate: 85.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 8.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.42 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.6 / Num. unique all: 2387 / Rsym value: 0.466 / % possible all: 100

-
Processing

Software
NameClassification
d*TREKdata scaling
CNSrefinement
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F42, 2esk

2f42

2esk


Resolution: 2.9→53.23 Å / Isotropic thermal model: anisotropic / Cross valid method: thoughout / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1089 -random
Rwork0.24 ---
all-24314 --
obs-22661 93.2 %-
Displacement parametersBiso mean: 65 Å2
Baniso -1Baniso -2Baniso -3
1--9.69 Å20 Å20 Å2
2--25.88 Å20 Å2
3----16.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.84 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 2.9→53.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3518 0 3 4 3525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.038
RfactorNum. reflection% reflection
Rfree0.479 161 -
Rwork0.412 --
obs-3193 84.4 %

+
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