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- PDB-2kdf: NMR structure of minor S5a (196-306):K48 linked diubiquitin species -

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Basic information

Entry
Database: PDB / ID: 2kdf
TitleNMR structure of minor S5a (196-306):K48 linked diubiquitin species
Components
  • 26S proteasome non-ATPase regulatory subunit 4
  • Ubiquitin
KeywordsPROTEIN BINDING / protein complex / ubiquitin interacting motifs / Cytoplasm / Nucleus / Phosphoprotein / Ubl conjugation / Alternative splicing / Proteasome
Function / homology
Function and homology information


: / : / protein modification process => GO:0036211 / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Proteasome assembly / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination ...: / : / protein modification process => GO:0036211 / proteasome accessory complex / proteasome regulatory particle, base subcomplex / Proteasome assembly / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / polyubiquitin modification-dependent protein binding / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Maturation of protein E / Maturation of protein E / cytosolic ribosome / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Regulation of innate immune responses to cytosolic DNA / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / proteasome complex / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
Similarity search - Function
: / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A ...: / Ubiquitin interaction motif / Proteasome subunit Rpn10 / Ubiquitin-interacting motif. / von Willebrand factor type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / von Willebrand factor A-like domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / 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
Polyubiquitin-C / 26S proteasome non-ATPase regulatory subunit 4 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsZhang, N. / Wang, Q. / Ehlinger, A. / Randles, L. / Lary, J.W. / Kang, Y. / Haririnia, A. / Cole, J.L. / Fushman, D. / Walters, K.J.
CitationJournal: Mol.Cell / Year: 2009
Title: Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.
Authors: Zhang, N. / Wang, Q. / Ehlinger, A. / Randles, L. / Lary, J.W. / Kang, Y. / Haririnia, A. / Storaska, A.J. / Cole, J.L. / Fushman, D. / Walters, K.J.
History
DepositionJan 6, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,9813
Polymers28,9813
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)7 / 30structures 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 S5A / Rpn10 / Multiubiquitin chain-binding protein / ...26S proteasome regulatory subunit S5A / Rpn10 / Multiubiquitin chain-binding protein / Antisecretory factor 1 / ASF / AF


Mass: 11826.878 Da / Num. of mol.: 1 / Fragment: UNP residues 196-306, S5a fragment
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 Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1, UBA52, UBCEP2, UBB, UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P62988, UniProt: P0CG48*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
2223D 1H-13C NOESY
2333D 13C-filtered 1H-13C NOESY
2443D 13C-filtered 1H-13C NOESY
2553D 13C-filtered 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 15N; U-50% 2H] S5a (196-306)-1, 1.2 mM K48 linked diubiquitin-2, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C] S5a (196-306)-3, 1.5 mM K48 linked diubiquitin-4, 100% D2O100% D2O
30.5 mM [U-100% 13C of the proximal Ub; natural abundance of the distal subunit] K48 linked diubiquitin-5, 1.0 mM S5a (196-306)-6, 100% D2O100% D2O
40.5 mM [U-100% 13C of the distal subunit; natural abundance of the proximal Ub] K48 linked diubiquitin-7, 1.0 mM S5a (196-306)-8, 100% D2O100% D2O
50.4 mM [U-100% 13C] S5a (196-306)-9, 1.2 mM [U-100% 2H of the proximal Ub; natural abundance of the distal subunit] K48 linked diubiquitin-10, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMS5a (196-306)-1[U-100% 15N; U-50% 2H]1
1.2 mMK48 linked diubiquitin-21
0.5 mMS5a (196-306)-3[U-100% 13C]2
1.5 mMK48 linked diubiquitin-42
0.5 mMK48 linked diubiquitin-5[U-100% 13C of the proximal Ub; natural abundance of the distal subunit]3
1.0 mMS5a (196-306)-63
0.5 mMK48 linked diubiquitin-7[U-100% 13C of the distal subunit; natural abundance of the proximal Ub]4
1.0 mMS5a (196-306)-84
0.4 mMS5a (196-306)-9[U-100% 13C]5
1.2 mMK48 linked diubiquitin-10[U-100% 2H of the proximal Ub; natural abundance of the distal subunit]5
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM NaPO4; 100 mM NaCl 6.5ambient 298 K
220 mM NaPO4; 50 mM NaCl 6.5ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
X-PLORBrungerstructure solution
X-PLORBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 7

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