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- PDB-1q0w: Solution structure of Vps27 amino-terminal UIM-ubiquitin complex -

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Basic information

Entry
Database: PDB / ID: 1q0w
TitleSolution structure of Vps27 amino-terminal UIM-ubiquitin complex
Components
  • Ubiquitin
  • Vacuolar protein sorting-associated protein VPS27
KeywordsTRANSPORT PROTEIN / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


positive regulation of protein maturation / microlipophagy / : / : / : / : / : / Regulation of TP53 Degradation / ESCRT-0 complex / Josephin domain DUBs ...positive regulation of protein maturation / microlipophagy / : / : / : / : / : / Regulation of TP53 Degradation / ESCRT-0 complex / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling / Aggrephagy / Pexophagy / Regulation of pyruvate metabolism / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / microautophagy / protein retention in Golgi apparatus / ABC-family proteins mediated transport / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / E3 ubiquitin ligases ubiquitinate target proteins / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ATP export / multivesicular body sorting pathway / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / protein targeting to vacuole / Translesion Synthesis by POLH / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Termination of translesion DNA synthesis / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / phosphatidylinositol-3-phosphate binding / Negative regulators of DDX58/IFIH1 signaling / cellular response to nitrogen starvation / vacuolar membrane / K48-linked polyubiquitin modification-dependent protein binding / Formation of the ternary complex, and subsequently, the 43S complex / K63-linked polyubiquitin modification-dependent protein binding / Ribosomal scanning and start codon recognition / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Formation of TC-NER Pre-Incision Complex / Major pathway of rRNA processing in the nucleolus and cytosol / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / Antigen processing: Ubiquitination & Proteasome degradation / protein secretion / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / ribosomal large subunit export from nucleus / Ub-specific processing proteases / ubiquitin binding / modification-dependent protein catabolic process / protein tag activity / peroxisome / ribosome biogenesis / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / endosome / endosome membrane / protein ubiquitination / structural constituent of ribosome / protein domain specific binding / protein heterodimerization activity / ubiquitin protein ligase binding / protein-containing complex / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 ...: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / ENTH/VHS / Ubiquitin interaction motif / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger, FYVE/PHD-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin / Vacuolar protein sorting-associated protein 27 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
AuthorsSwanson, K.A. / Kang, R.S. / Stamenova, S.D. / Hicke, L. / Radhakrishnan, I.
CitationJournal: Embo J. / Year: 2003
Title: Solution Structure of Vps27 UIM-Ubiquitin Complex Important for Endosomal Sorting and Receptor Downregulation
Authors: Swanson, K.A. / Kang, R.S. / Stamenova, S.D. / Hicke, L. / Radhakrishnan, I.
History
DepositionJul 17, 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 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Author determined secondary structure
Remark 700SHEET Author determined secondary structure

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein VPS27
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)11,3932
Polymers11,3932
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80The submitted conformers are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Vacuolar protein sorting-associated protein VPS27


Mass: 2824.103 Da / Num. of mol.: 1 / Fragment: Amino-terminal UIM, residues 256 to 278 / Source method: obtained synthetically
Details: The sequence was synthesized using a peptide synthesizer. The sequence contains a non-native tyrosine residue at the amino-terminus (residue number 255). The sequence occurs naturally in S. Cerevisiae.
References: UniProt: P40343
#2: Protein Ubiquitin


Mass: 8568.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: (UBI1 OR RPL40A OR YIL148W) AND (UBI2 OR RPL40B OR YKR094C) AND (UBI3 OR RPS31 OR YLR167W OR L9470.14) AND (UBI4 OR SCD2 OR YLL039C)
Plasmid: pET3-a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61864, UniProt: P0CG63*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D double half-filtered NOESY
1323D 13C-separated NOESY
1422D double half-filtered NOESY
1523D 13C-filtered,13C-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM90% H2O/10% D2O
21 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM100% D2O
Sample conditionsIonic strength: 20 mM sodium phosphate, pH 6.0, 0.2% NaN3 / pH: 6 / Pressure: 1 atm / Temperature: 298 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 spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVarian Instrumentscollection
Felix98Accelrysdata analysis
CNS1.1Brunger et al.refinement
ARIA1.2Linge and Nilgesrefinement
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2138 DISTANCE RESTRAINTS, INCLUDING 2062 NOE-DERIVED DISTANCE RESTRAINTS [1625 UNAMBIGUOUS AND 437 AMBIGUOUS RESTRAINTS], 76 HYDROGEN BONDING DISTANCE ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2138 DISTANCE RESTRAINTS, INCLUDING 2062 NOE-DERIVED DISTANCE RESTRAINTS [1625 UNAMBIGUOUS AND 437 AMBIGUOUS RESTRAINTS], 76 HYDROGEN BONDING DISTANCE RESTRAINTS, AND 112 TORSION ANGLE RESTRAINTS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformers are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
Conformers calculated total number: 80 / Conformers submitted total number: 20

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