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- PDB-3r42: Crystal structure of the yeast vps23 UEV domain in complex with a... -

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Basic information

Entry
Database: PDB / ID: 3r42
TitleCrystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide
Components
  • Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
  • Vacuolar protein sorting-associated protein 27
KeywordsPROTEIN TRANSPORT / endosomal sorting / ESCRT
Function / homology
Function and homology information


negative regulation of protein polyubiquitination / microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / ESCRT I complex / microautophagy / ATP export / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...negative regulation of protein polyubiquitination / microlipophagy / positive regulation of protein maturation / ESCRT-0 complex / ESCRT I complex / microautophagy / ATP export / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / protein targeting to membrane / reticulophagy / vacuolar membrane / endosome to lysosome transport / protein secretion / ubiquitin binding / protein modification process / cytoplasmic side of plasma membrane / late endosome membrane / endosome membrane / endosome / protein heterodimerization activity / protein domain specific binding / protein-containing complex / metal ion binding / cytosol
Similarity search - Function
: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / UEV domain / UEV domain profile. / ESCRT assembly domain ...: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / UEV domain / UEV domain profile. / ESCRT assembly domain / 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 Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease / Vacuolar protein sorting-associated protein 27
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.866 Å
AuthorsRen, X. / Hurley, J.H.
CitationJournal: Embo J. / Year: 2011
Title: Structural basis for endosomal recruitment of ESCRT-I by ESCRT-0 in yeast.
Authors: Ren, X. / Hurley, J.H.
History
DepositionMar 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 27


Theoretical massNumber of molelcules
Total (without water)19,0922
Polymers19,0922
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-4 kcal/mol
Surface area9380 Å2
MethodPISA
2
A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 27

A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 27


Theoretical massNumber of molelcules
Total (without water)38,1834
Polymers38,1834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3610 Å2
ΔGint-19 kcal/mol
Surface area17010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.200, 142.381, 32.065
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-217-

HOH

21A-222-

HOH

31A-223-

HOH

41A-266-

HOH

51A-267-

HOH

61A-297-

HOH

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Components

#1: Protein Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease / ESCRT-I complex subunit VPS23 / Vacuolar protein sorting-associated protein 23


Mass: 18009.535 Da / Num. of mol.: 1 / Fragment: N-terminal UEV domain (UNP residues 1-160) / Mutation: C133A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: STP22, VPS23, YCL008C, YCL8C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25604
#2: Protein/peptide Vacuolar protein sorting-associated protein 27 / VPS27 / Golgi retention defective protein 11


Mass: 1082.120 Da / Num. of mol.: 1 / Fragment: PSDP peptide (UNP residues 445-453) / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40343
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 0.2 M sodium phosphate monobasic, 20% PEG3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 29, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 18396 / Num. obs: 17866 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 14.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.9 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
autoBUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R3Q

3r3q


Resolution: 1.866→30.973 Å / SU ML: 0.16 / σ(F): 0.12 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 900 5.04 %RANDOM
Rwork0.1825 ---
obs0.1835 17866 95.57 %-
all-18396 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.74 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1684 Å2-0 Å2-0 Å2
2---2.0505 Å2-0 Å2
3----2.118 Å2
Refinement stepCycle: LAST / Resolution: 1.866→30.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 0 151 1446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071335
X-RAY DIFFRACTIONf_angle_d1.1131831
X-RAY DIFFRACTIONf_dihedral_angle_d15.121480
X-RAY DIFFRACTIONf_chiral_restr0.074207
X-RAY DIFFRACTIONf_plane_restr0.006236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8663-1.98330.23411420.18042405X-RAY DIFFRACTION83
1.9833-2.13640.22671470.1762787X-RAY DIFFRACTION96
2.1364-2.35130.2071520.17342802X-RAY DIFFRACTION97
2.3513-2.69130.21911460.18082902X-RAY DIFFRACTION98
2.6913-3.39010.21971700.18152943X-RAY DIFFRACTION100
3.3901-30.97760.17021430.18353127X-RAY DIFFRACTION100

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