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- PDB-1yx4: Structure of S5a bound to monoubiquitin provides a model for poly... -

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Basic information

Entry
Database: PDB / ID: 1yx4
TitleStructure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition
Components26S proteasome non-ATPase regulatory subunit 4
KeywordsHYDROLASE / polyubiquitin / proteasome / S5a / UIM
Function / homology
Function and homology information


proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / polyubiquitin modification-dependent protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin ...proteasome accessory complex / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / polyubiquitin modification-dependent protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / 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 / 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 / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / Ub-specific processing proteases / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Helix Hairpins - #3990 / : / Ubiquitin interaction motif / 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 ...Helix Hairpins - #3990 / : / Ubiquitin interaction motif / 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 / von Willebrand factor A-like domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, Q. / Young, P. / Walters, K.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure of S5a bound to monoubiquitin provides a model for polyubiquitin recognition
Authors: Wang, Q. / Young, P. / Walters, K.J.
History
DepositionFeb 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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
Remark 650Helix Determination Method: Author provided

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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


Theoretical massNumber of molelcules
Total (without water)14,3611
Polymers14,3611
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)15 / 15back calculated data agree with experimental NOESY spectrum
RepresentativeModel #10lowest 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 / AF / ASF


Mass: 14360.612 Da / Num. of mol.: 1 / Fragment: (poly)ubiquitin binding region
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
2213D 15N-separated NOESY
1313D 13C-separated NOESY
1412D NOESY
2512D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.35 mM S5a U-15N, 13C20 mM phosphate buffer pH 6.5, 100 mM NaCl, 10% D2O
21 mM S5a U-15N20 mM phosphate buffer pH 6.5, 100 mM NaCl, 10% D2O
30.5 mM S5a unlabeled20 mM phosphate buffer pH 6.5, 100 mM NaCl, 10% D2O
40.5 mM S5a U-N15 and 50% Deuterated20 mM phosphate buffer pH 6.5, 100 mM NaCl, 10% D2O
51 mM S5a U-C1320 mM phosphate buffer pH 6.5, 100 mM NaCl, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 6.5 1 atm298 K
2100 mM NaCl 6.5 1 atm283 K

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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
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionClassification
X-PLOR3.851structure solution
NMRPipedata analysis
X-PLOR3.851refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 15 / Conformers submitted total number: 15

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