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- PDB-1mn3: Cue domain of yeast Vps9p -

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Basic information

Entry
Database: PDB / ID: 1mn3
TitleCue domain of yeast Vps9p
ComponentsVacuolar protein sorting-associated protein VPS9
KeywordsPROTEIN TRANSPORT / Ubiquitin
Function / homology
Function and homology information


RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / Golgi to endosome transport / protein localization to endosome / late endosome to vacuole transport via multivesicular body sorting pathway / protein targeting to vacuole / endocytic vesicle / guanyl-nucleotide exchange factor activity / ubiquitin binding / small GTPase binding ...RAB GEFs exchange GTP for GDP on RABs / vacuole inheritance / Golgi to endosome transport / protein localization to endosome / late endosome to vacuole transport via multivesicular body sorting pathway / protein targeting to vacuole / endocytic vesicle / guanyl-nucleotide exchange factor activity / ubiquitin binding / small GTPase binding / early endosome / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 9, CUE domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / CUE domain ...Vacuolar protein sorting-associated protein 9, CUE domain / RABX5, catalytic core helical domain / Domain of unknown function (DUF5601) / Vacuolar protein sorting-associated protein 9-like / VPS9 domain / VPS9 domain superfamily / Vacuolar sorting protein 9 (VPS9) domain / VPS9 domain profile. / Domain present in VPS9 / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ubiquitin-associated (UBA) domain / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsPrag, G. / Misra, S. / Jones, E. / Ghirlando, R. / Davies, B.A. / Horazdovsky, B.F. / Hurley, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Mechanism of Ubiquitin Recognition by the CUE Domain of Vps9p
Authors: Prag, G. / Misra, S. / Jones, E.A. / Ghirlando, R. / Davies, B.A. / Horazdovsky, B.F. / Hurley, J.H.
History
DepositionSep 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein VPS9


Theoretical massNumber of molelcules
Total (without water)6,2231
Polymers6,2231
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Vacuolar protein sorting-associated protein VPS9

A: Vacuolar protein sorting-associated protein VPS9


Theoretical massNumber of molelcules
Total (without water)12,4462
Polymers12,4462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area1740 Å2
ΔGint-22 kcal/mol
Surface area7490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.487, 70.487, 61.384
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Vacuolar protein sorting-associated protein VPS9


Mass: 6222.829 Da / Num. of mol.: 1 / Fragment: Cue domain (residues 398-451) / Mutation: G440E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS9 / Plasmid: pHis-parallel2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Rosetta / References: UniProt: P54787
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.54 Å3/Da / Density % sol: 65.21 %
Description: The number of unique reflections observed include Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium Sulfate, Tris buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mg/mlprotein1drop
250 mM1dropNaCl
320 mMTris1droppH7.7
410 mMdithiothreitol1drop
51.9-2.1 Mammonium sulfate1reservoir
6100 mMTris-HCl1reservoirpH8.2-8.8

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.95645,0.97910,0.97924
DetectorType: SBC-2 / Detector: CCD / Date: Jul 13, 2002
RadiationMonochromator: Sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.956451
20.97911
30.979241
ReflectionResolution: 2.3→50 Å / Num. all: 7562 / Num. obs: 7325 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 24.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 39.5
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 6.8 / Num. unique all: 415 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 4327 / Redundancy: 23.5 % / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 99.8 % / Num. unique obs: 415 / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 6.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→43.29 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 763 10.4 %RANDOM
Rwork0.244 ---
all-7562 --
obs-7325 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.9679 Å2 / ksol: 0.3658 e/Å3
Displacement parametersBiso mean: 42.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å25.75 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å-
Refinement stepCycle: LAST / Resolution: 2.3→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms425 0 0 31 456
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it2.892
X-RAY DIFFRACTIONc_scbond_it3.252
X-RAY DIFFRACTIONc_scangle_it4.362.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 91 8 %
Rwork0.302 1043 -
obs-1043 88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 43.4 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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