[English] 日本語
Yorodumi
- PDB-5egg: Crystal structure of human ubiquitin-conjugating enzyme UBCH5C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5egg
TitleCrystal structure of human ubiquitin-conjugating enzyme UBCH5C
ComponentsUbiquitin-conjugating enzyme E2 D3
KeywordsTRANSFERASE / BIQUITIN-CONJUGATING ENZYME
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination ...(E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein monoubiquitination / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / protein autoubiquitination / ubiquitin ligase complex / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / protein modification process / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / endosome membrane / DNA repair / apoptotic process / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsZhu, L. / Li, H. / Wu, F. / Zhu, J.
Funding support China, 1items
OrganizationGrant numberCountry
the National Natural Science Foundation of China81302697 China
CitationJournal: Acta Pharm Sin B / Year: 2017
Title: Structural analysis of recombinant human ubiquitin-conjugating enzyme UbcH5c
Authors: Wu, F. / Zhu, J. / Li, H. / Zhu, L.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D3


Theoretical massNumber of molelcules
Total (without water)17,7801
Polymers17,7801
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8160 Å2
Unit cell
Length a, b, c (Å)28.170, 66.280, 76.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2 D3 / UBIQUITIN-CONJUGATING ENZYME UBCH5C / (E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ...UBIQUITIN-CONJUGATING ENZYME UBCH5C / (E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


Mass: 17780.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D3, UBC5C, UBCH5C / Production host: Escherichia coli (E. coli)
References: UniProt: P61077, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2% v/v Tacsimate pH 4.0, 0.1 M Sodium acetate trihydrate pH 4.6, 16% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.76→30.42 Å / Num. obs: 14797 / % possible obs: 99.47 % / Redundancy: 13.7 % / Net I/σ(I): 5.5
Reflection shellResolution: 1.76→1.86 Å / Num. unique all: 2116

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
AUTOMARphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X23

1x23


Resolution: 1.76→30.42 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.81 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 750 5.07 %
Rwork0.206 --
obs0.2082 14797 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 0 67 1245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111213
X-RAY DIFFRACTIONf_angle_d1.3161654
X-RAY DIFFRACTIONf_dihedral_angle_d12.903457
X-RAY DIFFRACTIONf_chiral_restr0.054178
X-RAY DIFFRACTIONf_plane_restr0.008216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.89590.31341620.23852738X-RAY DIFFRACTION100
1.8959-2.08660.27811650.22552735X-RAY DIFFRACTION100
2.0866-2.38850.25621610.20912804X-RAY DIFFRACTION100
2.3885-3.00880.26171340.21422832X-RAY DIFFRACTION100
3.0088-30.42880.22711280.19162938X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -12.5398 Å / Origin y: -20.744 Å / Origin z: 14.7688 Å
111213212223313233
T0.1567 Å2-0.0379 Å20.0204 Å2-0.1773 Å2-0.0188 Å2--0.1251 Å2
L0.8544 °21.266 °20.0616 °2-4.6128 °2-1.1412 °2--0.8007 °2
S-0.271 Å °0.2088 Å °-0.0199 Å °-0.393 Å °0.2908 Å °-0.1912 Å °0.0489 Å °-0.1435 Å °-0.0277 Å °
Refinement TLS groupSelection details: all

+
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