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- PDB-2pjw: The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquit... -

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Basic information

Entry
Database: PDB / ID: 2pjw
TitleThe Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting
Components
  • Uncharacterized protein YHL002W
  • Vacuolar protein sorting-associated protein 27
KeywordsENDOCYTOSIS/EXOCYTOSIS / GAT domain / Core complex / Doamin Swap / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


positive regulation of protein maturation / microlipophagy / ESCRT-0 complex / RHOU GTPase cycle / microautophagy / protein retention in Golgi apparatus / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ATP export / multivesicular body sorting pathway / protein targeting to vacuole ...positive regulation of protein maturation / microlipophagy / ESCRT-0 complex / RHOU GTPase cycle / microautophagy / protein retention in Golgi apparatus / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ATP export / 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 / cellular response to nitrogen starvation / vacuolar membrane / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / protein secretion / phosphatidylinositol binding / ubiquitin binding / endosome / endosome membrane / protein heterodimerization activity / protein domain specific binding / protein-containing complex / zinc ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1940 / : / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1940 / : / 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. / SH3 domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Zinc finger, FYVE/PHD-type / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Class E vacuolar protein-sorting machinery protein HSE1 / Vacuolar protein sorting-associated protein 27
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / TWO WAVELENGTH MAD / Resolution: 3.01 Å
AuthorsPrag, G. / Hurley, J.H.
Citation
Journal: Dev.Cell / Year: 2007
Title: The Vps27/Hse1 Complex Is a GAT Domain-Based Scaffold for Ubiquitin-Dependent Sorting.
Authors: Prag, G. / Watson, H. / Kim, Y.C. / Beach, B.M. / Ghirlando, R. / Hummer, G. / Bonifacino, J.S. / Hurley, J.H.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structural mechanism for ubiquitinated-cargo recognition by the Golgi-localized, {gamma}-ear-containing, ADP-ribosylation-factor-binding proteins
Authors: Prag, G. / Lee, S. / Mattera, R. / Arighi, C.N. / Beach, B.M. / Bonifacino, J.S. / Hurley, J.H.
History
DepositionApr 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Uncharacterized protein YHL002W
V: Vacuolar protein sorting-associated protein 27


Theoretical massNumber of molelcules
Total (without water)20,8202
Polymers20,8202
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-39 kcal/mol
Surface area10730 Å2
MethodPISA
2
H: Uncharacterized protein YHL002W
V: Vacuolar protein sorting-associated protein 27

H: Uncharacterized protein YHL002W
V: Vacuolar protein sorting-associated protein 27


Theoretical massNumber of molelcules
Total (without water)41,6414
Polymers41,6414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area10700 Å2
ΔGint-98 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.400, 62.400, 94.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Uncharacterized protein YHL002W


Mass: 10049.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: hse1 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P38753
#2: Protein Vacuolar protein sorting-associated protein 27


Mass: 10770.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS27, GRD11 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P40343
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.91 %
Description: The structure factor file contains Friedel pairs.
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 8.85
Details: 1.1-1.4 M ammonium sulfate, 0.1 M Tris-HCl. Then micro-seeding into 1.25 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.85, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979493, 0.972425
DetectorDetector: CCD / Date: Jul 12, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794931
20.9724251
ReflectionResolution: 3.01→46.92 Å / Num. obs: 7506 / Redundancy: 4.1 % / Rsym value: 0.052 / Net I/σ(I): 18.1
Reflection shellResolution: 3.01→3.14 Å

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: TWO WAVELENGTH MAD / Resolution: 3.01→46.92 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 276902.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED. The Friedel pairs were used for phasing.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 381 5.1 %RANDOM
Rwork0.222 ---
obs0.222 7506 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.289 Å2 / ksol: 0.370494 e/Å3
Displacement parametersBiso mean: 70.7 Å2
Baniso -1Baniso -2Baniso -3
1-14.9 Å213.81 Å20 Å2
2--14.9 Å20 Å2
3----29.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.01→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 0 29 1458
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 39 4.5 %
Rwork0.4 831 -
obs--64.2 %

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