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- PDB-1q0v: Solution Structure of Tandem UIMs of Vps27 -

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Basic information

Entry
Database: PDB / ID: 1q0v
TitleSolution Structure of Tandem UIMs of Vps27
Componentshydrophilic protein; has cysteine rich putative zinc finger essential for function; Vps27pHydrophile
KeywordsTRANSPORT BINDING / Stable / non-interacting alpha-helices
Function / homology
Function and homology information


microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / microautophagy / ATP export / protein retention in Golgi apparatus / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / multivesicular body sorting pathway / late endosome to vacuole transport ...microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / microautophagy / ATP export / protein retention in Golgi apparatus / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / multivesicular body sorting pathway / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / vacuolar membrane / protein secretion / ubiquitin binding / endosome membrane / endosome / protein heterodimerization activity / protein domain specific binding / protein-containing complex / metal ion binding
Similarity search - Function
Helix Hairpins - #100 / : / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain / VHS domain profile. ...Helix Hairpins - #100 / : / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Ubiquitin interaction motif / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Helix Hairpins / Helix non-globular / Special / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 27
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 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hydrophilic protein; has cysteine rich putative zinc finger essential for function; Vps27p


Theoretical massNumber of molelcules
Total (without water)9,3701
Polymers9,3701
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)20 / 80the submitted conformer models are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
RepresentativeModel #1the structure with the lowest restraint energy.

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Components

#1: Protein hydrophilic protein; has cysteine rich putative zinc finger essential for function; Vps27p / Hydrophile


Mass: 9370.256 Da / Num. of mol.: 1 / Fragment: Tandem UIM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: vps27 / Plasmid: pET30 derivative / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40343

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Vps27 UIM U-15N90% H2O/10% D2O
21 mM Vps27 UIM U-15N,U-13C100% D2O
Sample conditionsIonic strength: 20 mM sodium phosphate, pH 6.0, 0.2% NaN3 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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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 858 DISTANCE RESTRAINTS, INCLUDING 808 NOE-DERIVED DISTANCE RESTRAINTS [412 UNAMBIGUOUS AND 396 AMBIGUOUS RESTRAINTS], 50 HYDROGEN BONDING DISTANCE ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 858 DISTANCE RESTRAINTS, INCLUDING 808 NOE-DERIVED DISTANCE RESTRAINTS [412 UNAMBIGUOUS AND 396 AMBIGUOUS RESTRAINTS], 50 HYDROGEN BONDING DISTANCE RESTRAINTS, AND 66 TORSION ANGLE RESTRAINTS.
NMR representativeSelection criteria: the structure with the lowest restraint energy.
NMR ensembleConformer selection criteria: the submitted conformer models 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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