[English] 日本語
Yorodumi
- PDB-6mun: Structure of hRpn10 bound to UBQLN2 UBL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mun
TitleStructure of hRpn10 bound to UBQLN2 UBL
Components
  • 26S proteasome non-ATPase regulatory subunit 4
  • Ubiquilin-2
KeywordsSTRUCTURAL PROTEIN / proteasome / shuttle factor / Complex
Function / homology
Function and homology information


negative regulation of G protein-coupled receptor internalization / negative regulation of clathrin-dependent endocytosis / positive regulation of ERAD pathway / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of autophagosome assembly / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis ...negative regulation of G protein-coupled receptor internalization / negative regulation of clathrin-dependent endocytosis / positive regulation of ERAD pathway / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of autophagosome assembly / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / autophagosome assembly / autophagosome / polyubiquitin modification-dependent protein binding / regulation of macroautophagy / ERAD pathway / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / molecular condensate scaffold activity / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / Ub-specific processing proteases / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / Ubiquitin interaction motif / Ubiquitin-interacting motif. / UBA/TS-N domain / von Willebrand factor type A domain / Ubiquitin associated domain / Ubiquitin-associated domain ...: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / Ubiquitin interaction motif / Ubiquitin-interacting motif. / UBA/TS-N domain / von Willebrand factor type A domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / UBA-like superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / von Willebrand factor A-like domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 4 / Ubiquilin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, X. / Walters, K.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIA BC011490 United States
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Structure of hRpn10 Bound to UBQLN2 UBL Illustrates Basis for Complementarity between Shuttle Factors and Substrates at the Proteasome.
Authors: Chen, X. / Ebelle, D.L. / Wright, B.J. / Sridharan, V. / Hooper, E. / Walters, K.J.
History
DepositionOct 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 26S proteasome non-ATPase regulatory subunit 4
B: Ubiquilin-2
C: Ubiquilin-2


Theoretical massNumber of molelcules
Total (without water)29,3553
Polymers29,3553
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1900 Å2
ΔGint-13 kcal/mol
Surface area18320 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory ...26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory factor 1 / ASF / Multiubiquitin chain-binding protein


Mass: 11826.878 Da / Num. of mol.: 1 / Fragment: UNP Residues 196-306
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4, MCB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55036
#2: Protein Ubiquilin-2 / Chap1 / DSK2 homolog / Protein linking IAP with cytoskeleton 2 / hPLIC-2 / Ubiquitin-like product Chap1/Dsk2


Mass: 8764.189 Da / Num. of mol.: 2 / Fragment: UNP Residues 26-103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBQLN2, N4BP4, PLIC2, HRIHFB2157 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHD9

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
132isotropic12D 1H-13C HSQC aliphatic
142isotropic13D 1H-13C NOESY aliphatic
152isotropic12D 1H-13C HSQC aliphatic
1112isotropic13D 1H-13C half-filter NOESY
1103isotropic12D 1H-15N HSQC
193isotropic13D 1H-15N NOESY
184isotropic32D 1H-15N HSQC
174isotropic33D 1H-15N NOESY
165isotropic12D 1H-13C HSQC aliphatic
1155isotropic13D 1H-13C NOESY aliphatic
1145isotropic22D 1H-13C HSQC aliphatic
1135isotropic23D 1H-13C half-filter NOESY
1126isotropic22D 1H-13C HSQC aliphatic
1166isotropic23D 1H-13C half-filter NOESY
1175isotropic32D 1H-13C HSQC aliphatic
1185isotropic33D (H)CCH-TOCSY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM [U-100% 15N] hRpn10 196-306, 1.38 mM UBQLN2 UBL, 20 mM NaPO4, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O15N-hRpn10 196-306:UBQLN2 UBL=1:2.3 in 95% H2O95% H2O/5% D2O
solution20.6 mM [U-100% 13C] hRpn10 196-306, 1.38 mM UBQLN2 UBL, 20 mM NaPO4, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 100% D2O13C-hRpn10 196-306:UBQLN2 UBL=1:2.3 in 100% D2O100% D2O
solution30.6 mM [U-100% 15N; U-100% 2H] hRpn10 196-306, 1.38 mM UBQLN2 UBL, 20 mM NaPO4, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O15N, 100%D-hRpn10 196-306:UBQLN2 UBL=1:2.3 in 95% H2O95% H2O/5% D2O
solution40.6 mM [U-100% 13C; U-100% 15N] UBQLN2 UBL, 0.6 mM hRpn10 196-306, 20 mM NaPO4, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 95% H2O/5% D2O15N, 13C-UBQLN2 UBL:hRpn10 196-306=1:1 in 95% H2O95% H2O/5% D2O
solution50.6 mM [U-100% 13C; U-100% 15N] UBQLN2 UBL, 0.6 mM hRpn10 196-306, 20 mM NaPO4, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 100% D2O15N, 13C-UBQLN2 UBL:hRpn10 196-306=1:1 in 100% D2O100% D2O
solution60.6 mM [U-100% 13C; U-100% 15N] UBQLN2 UBL, 20 mM NaPO4, 50 mM sodium chloride, 2 mM DTT, 0.1 % sodium azide, 100% D2O15N, 13C-UBQLN2 UBL free100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMhRpn10 196-306[U-100% 15N]1
1.38 mMUBQLN2 UBLnatural abundance1
20 mMNaPO4natural abundance1
50 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
0.1 %sodium azidenatural abundance1
0.6 mMhRpn10 196-306[U-100% 13C]2
1.38 mMUBQLN2 UBLnatural abundance2
20 mMNaPO4natural abundance2
50 mMsodium chloridenatural abundance2
2 mMDTTnatural abundance2
0.1 %sodium azidenatural abundance2
0.6 mMhRpn10 196-306[U-100% 15N; U-100% 2H]3
1.38 mMUBQLN2 UBLnatural abundance3
20 mMNaPO4natural abundance3
50 mMsodium chloridenatural abundance3
2 mMDTTnatural abundance3
0.1 %sodium azidenatural abundance3
0.6 mMUBQLN2 UBL[U-100% 13C; U-100% 15N]4
0.6 mMhRpn10 196-306natural abundance4
20 mMNaPO4natural abundance4
50 mMsodium chloridenatural abundance4
2 mMDTTnatural abundance4
0.1 %sodium azidenatural abundance4
0.6 mMUBQLN2 UBL[U-100% 13C; U-100% 15N]5
0.6 mMhRpn10 196-306natural abundance5
20 mMNaPO4natural abundance5
50 mMsodium chloridenatural abundance5
2 mMDTTnatural abundance5
0.1 %sodium azidenatural abundance5
0.6 mMUBQLN2 UBL[U-100% 13C; U-100% 15N]6
20 mMNaPO4natural abundance6
50 mMsodium chloridenatural abundance6
2 mMDTTnatural abundance6
0.1 %sodium azidenatural abundance6
Sample conditionsIonic strength: 50 mM / Label: 25 degree / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8501
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE7003

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxdata analysis
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

+
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://pdbjlvh1.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