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- PDB-1uel: Solution structure of ubiquitin-like domain of hHR23B complexed w... -

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Entry
Database: PDB / ID: 1uel
TitleSolution structure of ubiquitin-like domain of hHR23B complexed with ubiquitin-interacting motif of proteasome subunit S5a
Components
  • 26S proteasome non-ATPase regulatory subunit 4
  • UV excision repair protein RAD23 homolog B
KeywordsGENE REGULATION/protein binding / UBL / UIM / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / GENE REGULATION-protein binding COMPLEX
Function / homology
Function and homology information


XPC complex / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome accessory complex / proteasome regulatory particle, base subcomplex / cellular response to interleukin-7 / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome binding ...XPC complex / DNA damage sensor activity / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome accessory complex / proteasome regulatory particle, base subcomplex / cellular response to interleukin-7 / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome binding / polyubiquitin modification-dependent protein binding / embryonic organ development / proteasome complex / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / 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 / nucleotide-excision repair / 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 / DNA Damage Recognition in GG-NER / 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 / Formation of Incision Complex in GG-NER / 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 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / single-stranded DNA binding / ER-Phagosome pathway / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / molecular adaptor activity / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
cAMP-dependent Protein Kinase, Chain A - #40 / cAMP-dependent Protein Kinase, Chain A / 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. / : ...cAMP-dependent Protein Kinase, Chain A - #40 / cAMP-dependent Protein Kinase, Chain A / 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. / 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 / Helix non-globular / Special / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
UV excision repair protein RAD23 homolog B / 26S proteasome non-ATPase regulatory subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing procedure in CNS, further refined by AMBER 7
AuthorsFujiwara, K. / Tenno, T. / Jee, J.G. / Sugasawa, K. / Ohki, I. / Kojima, C. / Tochio, H. / Hiroaki, H. / Hanaoka, H. / Shirakawa, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure of the Ubiquitin-interacting Motif of S5a Bound to the Ubiquitin-like Domain of HR23B
Authors: Fujiwara, K. / Tenno, T. / Sugasawa, K. / Jee, J.G. / Ohki, I. / Kojima, C. / Tochio, H. / Hiroaki, H. / Hanaoka, F. / Shirakawa, M.
History
DepositionMay 19, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,9492
Polymers15,9492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100The submitted conformer models are the 20 structures with the lowest
Representative

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Components

#1: Protein UV excision repair protein RAD23 homolog B / hHR23B


Mass: 10750.396 Da / Num. of mol.: 1 / Fragment: ubiquitin-like domain (RESIDUES 1-95)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / References: UniProt: P54727
#2: Protein/peptide 26S proteasome non-ATPase regulatory subunit 4 / S5a / 26S proteasome regulatory subunit S5A


Mass: 5198.620 Da / Num. of mol.: 1 / Fragment: ubiquitin-interacting motif (RESIDUES 201-248)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / References: UniProt: P55036

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: U-15N, U-13C
Solvent system: 20mM potassium phosphate buffer (pH 6.8), 5mM KCl, 90% H2O, 10% D2O
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 DRXBrukerDRX8002

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Processing

NMR softwareName: Amber / Version: 7 / Classification: refinement
RefinementMethod: simulated annealing procedure in CNS, further refined by AMBER 7
Software ordinal: 1
Details: RESIDUES INCLUDING MET1 THROUGH THR75 OF HHR23B AND LEU278 THROUGH GLN 296 OF S5A ARE ORDERED IN SOLUTION, WHILE THE REST IS HIGHLY FLEXIBLE (BASED ON 1H-15N HETERONUCLEAR NOE ANALYSIS).
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest
Conformers calculated total number: 100 / Conformers submitted total number: 20

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