[English] 日本語
Yorodumi
- PDB-2mbb: Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mbb
TitleSolution Structure of the human Polymerase iota UBM1-Ubiquitin Complex
Components
  • Immunoglobulin G-binding protein G/DNA polymerase iota fusion protein
  • Polyubiquitin-B
KeywordsTRANSFERASE / SIGNALING PROTEIN / Polymerase iota / UBM / UBM1 / ubiquitin
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / IgG binding / symbiont entry into host cell via disruption of host cell envelope / virus tail / error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / damaged DNA binding ...symbiont entry into host cell via disruption of host cell glycocalyx / IgG binding / symbiont entry into host cell via disruption of host cell envelope / virus tail / error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nuclear speck / DNA repair / extracellular region / nucleoplasm / metal ion binding
Similarity search - Function
HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily ...HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / YSIRK Gram-positive signal peptide / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Pectin lyase fold / Pectin lyase fold/virulence factor / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Reverse transcriptase/Diguanylate cyclase domain / Roll / DNA/RNA polymerase superfamily / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin G-binding protein G / Tail fiber / DNA polymerase iota
Similarity search - Component
Biological speciesStreptococcus sp. 'group G' (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsWang, S. / Zhou, P.
CitationJournal: J.Biomol.Nmr / Year: 2014
Title: Sparsely-sampled, high-resolution 4-D omit spectra for detection and assignment of intermolecular NOEs of protein complexes.
Authors: Wang, S. / Zhou, P.
History
DepositionJul 29, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoglobulin G-binding protein G/DNA polymerase iota fusion protein
B: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)20,7962
Polymers20,7962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1593 Å2
ΔGint-8.6 kcal/mol
Surface area6321 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Antibody Immunoglobulin G-binding protein G/DNA polymerase iota fusion protein


Mass: 11994.217 Da / Num. of mol.: 1
Fragment: UNP P06654 residues 229-282, UNP Q9UNA4 residues 516-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G', Homo sapiens
Production host: Escherichia coli (E. coli) / References: UniProt: P06654, UniProt: Q9UNA4
#2: Protein Polyubiquitin-B / Ubiquitin


Mass: 8802.056 Da / Num. of mol.: 1 / Fragment: UNP P0CG47 residues 1-76
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

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1323D sparse-sampled HNCO
1423D sparse-sampled HNCA
1523D sparse-sampled HN(CA)CB
1623D sparse-sampled HN(CO)CA
1713D 1H-15N NOESY
1823D sparse-sampled HN(COCA)CB
1923D (HACA)CO(CA)NH
11023D sparse-sampled HA(CACO)NH
11123D sparse-sampled HA(CA)NH
11224D sparse-sampled HC(CO)NH-TOCSY
11324D sparse-sampled CHNH NOESY
11434D sparse-sampled CHCH NOESY
11544D sparse-sampled CHCH NOESY
11654D sparse-sampled CHCH NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
13 mM [U-100% 15N] GB1-UBM1, 3 mM [U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
23 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
33 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O100% D2O
43 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O100% D2O
53 mM GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3 mMGB1-UBM1-1[U-100% 15N]1
3 mMubiquitin-2[U-100% 15N]1
100 mMpotassium chloride-31
25 mMsodium phosphate-41
3 mMGB1-UBM1-5[U-100% 13C; U-100% 15N]2
3 mMubiquitin-6[U-100% 13C; U-100% 15N]2
100 mMpotassium chloride-72
25 mMsodium phosphate-82
3 mMGB1-UBM1-9[U-100% 13C; U-100% 15N]3
3 mMubiquitin-10[U-100% 13C; U-100% 15N]3
100 mMpotassium chloride-113
25 mMsodium phosphate-123
3 mMGB1-UBM1-13[U-100% 13C; U-100% 15N]4
3 mMubiquitin-144
100 mMpotassium chloride-154
25 mMsodium phosphate-164
3 mMGB1-UBM1-175
3 mMubiquitin-18[U-100% 13C; U-100% 15N]5
100 mMpotassium chloride-195
25 mMsodium phosphate-205
Sample conditionsIonic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
SCRUBCoggins and Zhouprocessing
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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