[English] 日本語
Yorodumi
- PDB-1j74: Crystal Structure of Mms2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j74
TitleCrystal Structure of Mms2
ComponentsMMS2
KeywordsUNKNOWN FUNCTION / Mms2 / Uev / Ubiquitin / Ubc / DNA repair
Function / homology
Function and homology information


error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / positive regulation of double-strand break repair / protein K63-linked ubiquitination / regulation of DNA repair / Nonhomologous End-Joining (NHEJ) ...error-free postreplication DNA repair / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / DNA damage tolerance / positive regulation of double-strand break repair / protein K63-linked ubiquitination / regulation of DNA repair / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Formation of Incision Complex in GG-NER / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / protein ubiquitination / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMoraes, T.F. / Edwards, R.A. / McKenna, S. / Pastushok, L. / Xiao, W. / Glover, J.N.M. / Ellison, M.J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2-hUbc13.
Authors: Moraes, T.F. / Edwards, R.A. / McKenna, S. / Pastushok, L. / Xiao, W. / Glover, J.N. / Ellison, M.J.
History
DepositionMay 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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: MMS2


Theoretical massNumber of molelcules
Total (without water)16,3811
Polymers16,3811
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.190, 54.540, 108.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein MMS2


Mass: 16380.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15819
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.9 Å3/Da / Density % sol: 35.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 6000, 25mM NaCl, 100mM citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20-24 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
250 mMHEPES1drop
375 mM1dropNaCl
41 mMEDTA1drop
50.5 mMdithiothreitol1drop
616 %(w/v)PEG60001reservoir
725 mM1reservoirNaCl
8100 mMcitrate1reservoir

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 21, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 9995 / Num. obs: 9973 / % possible obs: 97.9 % / Redundancy: 5.35 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 4.5 / Net I/σ(I): 37.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 20 / Num. unique all: 445 / Rsym value: 12.9 / % possible all: 87.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 53554

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J7D

1j7d


Resolution: 1.9→20 Å / Stereochemistry target values: CNS template
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 472 -RANDOM
Rwork0.2134 ---
all-10194 --
obs-9972 97.8 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 0 99 1207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2649
X-RAY DIFFRACTIONc_bond_d0.004885
LS refinement shellResolution: 1.9→1.98 Å
RfactorNum. reflection
Rfree0.3271 50
Rwork0.2564 -
obs-986
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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