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- PDB-6mun: Structure of hRpn10 bound to UBQLN2 UBL -

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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 autophagosome assembly / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Proteasome assembly / autophagosome assembly / polyubiquitin modification-dependent protein binding / regulation of macroautophagy ...negative regulation of G protein-coupled receptor internalization / negative regulation of clathrin-dependent endocytosis / positive regulation of ERAD pathway / regulation of autophagosome assembly / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Proteasome assembly / autophagosome assembly / polyubiquitin modification-dependent protein binding / regulation of macroautophagy / ERAD pathway / proteasome complex / autophagosome / molecular condensate scaffold activity / Cargo recognition for clathrin-mediated endocytosis / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ubiquilin-1-like domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / : / UBA/TS-N domain / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / von Willebrand factor type A domain ...Ubiquilin-1-like domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / : / UBA/TS-N domain / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / 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 / von Willebrand factor A-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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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

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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

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NMR measurement

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

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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

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