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- PDB-1p9d: High-resolution structure of the complex of HHR23A ubiquitin-like... -

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Basic information

Entry
Database: PDB / ID: 1p9d
TitleHigh-resolution structure of the complex of HHR23A ubiquitin-like domain and the C-terminal ubiquitin-interacting motif of proteasome subunit S5a
Components
  • 26S proteasome non-ATPase regulatory subunit 4
  • UV excision repair protein RAD23 homolog A
KeywordsREPLICATION / protein-peptide complex
Function / homology
Function and homology information


regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication ...regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome binding / ubiquitin-specific protease binding / polyubiquitin modification-dependent protein binding / positive regulation of viral genome replication / positive regulation of cell cycle / proteasome complex / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / ubiquitin binding / 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 / Degradation of DVL / Vpu mediated degradation of CD4 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / nucleotide-excision repair / Degradation of GLI1 by the proteasome / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / DNA Damage Recognition in GG-NER / Autodegradation of the E3 ubiquitin ligase COP1 / 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 / protein destabilization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / 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 / Formation of Incision Complex in GG-NER / Regulation of expression of SLITs and ROBOs / kinase binding / FCERI mediated NF-kB activation / Interleukin-1 signaling / Regulation of PTEN stability and activity / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / single-stranded DNA binding / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / molecular adaptor activity / Ub-specific processing proteases / intracellular membrane-bounded organelle / Golgi apparatus / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / Ubiquitin interaction motif / Ubiquitin-interacting motif. ...RAD23A/RAD23B, UBA1 domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / Ubiquitin interaction motif / Ubiquitin-interacting motif. / von Willebrand factor type A domain / UBA/TS-N 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-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
UV excision repair protein RAD23 homolog A / 26S proteasome non-ATPase regulatory subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMueller, T.D. / Feigon, J.
CitationJournal: Embo J. / Year: 2003
Title: Structural determinants for the binding of ubiquitin-like domains to the proteasome.
Authors: Mueller, T.D. / Feigon, J.
History
DepositionMay 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: 26S proteasome non-ATPase regulatory subunit 4
U: UV excision repair protein RAD23 homolog A


Theoretical massNumber of molelcules
Total (without water)13,8702
Polymers13,8702
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit S5A / Rpn10 / Multiubiquitin chain binding protein / ...26S proteasome regulatory subunit S5A / Rpn10 / Multiubiquitin chain binding protein / Antisecretory factor-1 / AF / ASF


Mass: 4916.343 Da / Num. of mol.: 1 / Fragment: C-terminal ubiquitin-interacting motif, PUBS2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4 OR MCB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P55036
#2: Protein UV excision repair protein RAD23 homolog A / HHR23A


Mass: 8953.532 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD23A / Production host: Escherichia coli (E. coli) / References: UniProt: P54725

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
12115N-,13C-filtered/edited 2D-NOESY
13215N-,13C-filtered/edited 2D-NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM S5a peptide unlabeled, 2mM ubiquitin-like domain of HHR23A U-15N,13C50mM sodium phosphate, 100mM sodium chloride, 5% D2O
22mM S5a peptide U-15N,13C, 2mM ubiquitin-like domain of HHR23A unlabeled50mM sodium phosphate, 100mM sodium chloride, 5% D2O
Sample conditionsIonic strength: 150mM / pH: 6.5 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Bruker Karlsruheprocessing
AURELIA2.8.9Neidigdata analysis
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2066 restraints, 1999 are NOE-derived distance restraints, of which 58 are intermolecular. For the S5a ubiquitin-interacting motif only the residues ...Details: The structures are based on a total of 2066 restraints, 1999 are NOE-derived distance restraints, of which 58 are intermolecular. For the S5a ubiquitin-interacting motif only the residues 270 to 301 were included in the structure calculations due to disorder of the flexible N- and C-termini.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 10

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