[English] 日本語
Yorodumi
- PDB-6if1: Crystal structure of Ube2K and K48-linked di-ubiquitin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6if1
TitleCrystal structure of Ube2K and K48-linked di-ubiquitin complex
Components
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 K
KeywordsLIGASE / complex
Function / homology
Function and homology information


free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of type I interferon-mediated signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / symbiont entry into host cell via disruption of host cell glycocalyx / positive regulation of peptidyl-threonine phosphorylation / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope ...free ubiquitin chain polymerization / regulation of proteasomal ubiquitin-dependent protein catabolic process / filopodium tip / positive regulation of type I interferon-mediated signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / symbiont entry into host cell via disruption of host cell glycocalyx / positive regulation of peptidyl-threonine phosphorylation / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / cellular response to interferon-beta / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Negative regulators of DDX58/IFIH1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / 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 / Ubiquitin-conjugating enzyme/RWD-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Helicase, Ruva Protein; domain 3 / Ubiquitin family / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tail fiber / Ubiquitin-conjugating enzyme E2 K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.466 Å
AuthorsLee, J.-G. / Youn, H.-S. / Lee, Y. / An, J.Y. / Park, K.R. / Kang, J.Y. / Lim, J.J. / Eom, S.H.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Crystal structure of the Ube2K/E2-25K and K48-linked di-ubiquitin complex provides structural insight into the mechanism of K48-specific ubiquitin chain synthesis.
Authors: Lee, J.G. / Youn, H.S. / Kang, J.Y. / Park, S.Y. / Kidera, A. / Yoo, Y.J. / Eom, S.H.
History
DepositionSep 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 K
B: Ubiquitin-conjugating enzyme E2 K
C: Ubiquitin
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)61,7874
Polymers61,7874
Non-polymers00
Water46826
1
A: Ubiquitin-conjugating enzyme E2 K
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)30,8932
Polymers30,8932
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-6 kcal/mol
Surface area14090 Å2
MethodPISA
2
B: Ubiquitin-conjugating enzyme E2 K
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)30,8932
Polymers30,8932
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-7 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.559, 38.792, 190.321
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2 K / E2 ubiquitin-conjugating enzyme K / Huntingtin-interacting protein 2 / HIP-2 / Ubiquitin carrier ...E2 ubiquitin-conjugating enzyme K / Huntingtin-interacting protein 2 / HIP-2 / Ubiquitin carrier protein / Ubiquitin-conjugating enzyme E2-25 kDa / Ubiquitin-conjugating enzyme E2-25K / Ubiquitin-protein ligase


Mass: 22316.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2K, HIP2, LIG / Production host: Escherichia coli (E. coli)
References: UniProt: P61086, E2 ubiquitin-conjugating enzyme
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10
Details: Tris-HCl, polyethylene glycol 3350, ammonium acetate.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.466→50 Å / Num. obs: 22344 / % possible obs: 99.8 % / Redundancy: 7.1 % / Net I/σ(I): 9.5
Reflection shellResolution: 2.47→2.51 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K9P

3k9p


Resolution: 2.466→47.58 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.03
RfactorNum. reflection% reflection
Rfree0.2356 1103 5.06 %
Rwork0.2152 --
obs0.2163 21808 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.466→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 0 26 4366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0254420
X-RAY DIFFRACTIONf_angle_d2.0195994
X-RAY DIFFRACTIONf_dihedral_angle_d27.3441682
X-RAY DIFFRACTIONf_chiral_restr0.174692
X-RAY DIFFRACTIONf_plane_restr0.019772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4662-2.57850.2571210.25152183X-RAY DIFFRACTION83
2.5785-2.71440.27481300.27122523X-RAY DIFFRACTION97
2.7144-2.88450.29571380.25642596X-RAY DIFFRACTION100
2.8845-3.10710.2641460.23772650X-RAY DIFFRACTION100
3.1071-3.41970.26421450.23822663X-RAY DIFFRACTION100
3.4197-3.91440.21551330.20712651X-RAY DIFFRACTION100
3.9144-4.93090.18961430.17822690X-RAY DIFFRACTION100
4.9309-47.5890.22721470.19452749X-RAY DIFFRACTION98

+
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