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- PDB-4uuy: Structural Identification of the Vps18 beta-propeller reveals a c... -

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Basic information

Entry
Database: PDB / ID: 4uuy
TitleStructural Identification of the Vps18 beta-propeller reveals a critical role in the HOPS complex stability and function.
ComponentsVACUOLAR MEMBRANE PROTEIN PEP3
KeywordsTRANSPORT PROTEIN / HOPS / MEMBRANE FUSION / VACUOLE / ENDOSOME
Function / homology
Function and homology information


CORVET complex / organelle fusion / HOPS complex / regulation of SNARE complex assembly / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole fusion, non-autophagic / Golgi to endosome transport / endosome organization / vacuole organization ...CORVET complex / organelle fusion / HOPS complex / regulation of SNARE complex assembly / vesicle tethering / regulation of vacuole fusion, non-autophagic / vacuole fusion, non-autophagic / Golgi to endosome transport / endosome organization / vacuole organization / vesicle docking involved in exocytosis / late endosome to vacuole transport / fungal-type vacuole membrane / intracellular protein transport / protein-macromolecule adaptor activity / early endosome membrane / endosome / metal ion binding / cytosol
Similarity search - Function
Pep3/Vps18/deep orange / Pep3/Vps18/deep orange beta-propeller domain / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile.
Similarity search - Domain/homology
Vacuolar membrane protein PEP3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.14 Å
AuthorsBehrmann, H. / Gohlke, U. / Heinemann, U.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Identification of the Vps18 Beta-Propeller Reveals a Critical Role in the Hops Complex Stability and Function.
Authors: Behrmann, H. / Lurick, A. / Kuhlee, A. / Balderhaar, H.K. / Brocker, C. / Kummel, D. / Engelbrecht-Vandre, S. / Gohlke, U. / Raunser, S. / Heinemann, U. / Ungermann, C.
History
DepositionAug 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VACUOLAR MEMBRANE PROTEIN PEP3
B: VACUOLAR MEMBRANE PROTEIN PEP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,75713
Polymers80,8112
Non-polymers94711
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-87.7 kcal/mol
Surface area28300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.250, 77.534, 84.508
Angle α, β, γ (deg.)90.00, 98.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9491, 0.004047, 0.3151), (0.005142, -1, -0.002644), (0.3151, 0.00413, -0.9491)
Vector: -5.48, 39.04, 32.92)

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Components

#1: Protein VACUOLAR MEMBRANE PROTEIN PEP3 / CARBOXYPEPTIDASE Y-DEFICIENT PROTEIN 3 / VACUOLAR MORPHOGENESIS PROTEIN 8 / VACUOLAR PROTEIN ...CARBOXYPEPTIDASE Y-DEFICIENT PROTEIN 3 / VACUOLAR MORPHOGENESIS PROTEIN 8 / VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 18 / VACUOLAR PROTEIN-TARGETING PROTEIN 18 / VPS18


Mass: 40405.297 Da / Num. of mol.: 2 / Fragment: BETA-PROPELLER, RESIDUES 2-348
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PQLINKH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: P27801
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsETHYLENE GLYCOL (EDO): SOLVENT GLYCEROL (GOL): SOLVENT SULPHATE (SO4): SOLVENT
Sequence detailsFRAGMENT AA2-348

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE
Crystal growDetails: 25 % (W/V) PEG 3350, 0.2 M (NH4)2SO4, 0.1 M BIS-TRIS, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.14→63.12 Å / Num. obs: 39106 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.14→43.31 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.945 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24445 2648 6.8 %RANDOM
Rwork0.20138 ---
obs0.20431 36420 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.035 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20.09 Å2
2---0.96 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.14→43.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5197 0 54 207 5458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195426
X-RAY DIFFRACTIONr_bond_other_d0.0030.025311
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9637348
X-RAY DIFFRACTIONr_angle_other_deg0.821312217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04224.816245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.744151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6851522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025951
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021243
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3311.7622576
X-RAY DIFFRACTIONr_mcbond_other1.3271.7612575
X-RAY DIFFRACTIONr_mcangle_it2.3562.6263221
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3262.0052850
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.143→2.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 175 -
Rwork0.287 2379 -
obs--88.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.88390.7341-0.0432.3807-0.33970.97250.00710.12380.1513-0.07390.06350.3265-0.1329-0.1194-0.07060.08850.00850.02980.0950.02880.08457.664536.90987.1405
21.02390.28670.08091.44450.25790.72260.02780.07890.0282-0.094-0.008-0.03660.0003-0.0069-0.01980.15170.01250.02570.09710.01420.06823.591822.44715.1077
36.01034.8848-1.876811.08850.15623.3858-0.21240.568-0.49690.06260.27450.81370.3065-0.8263-0.06220.0592-0.0223-0.00110.29620.01460.3682-5.5615.803829.7282
40.7734-0.0789-0.04661.3804-0.2090.81390.0519-0.0585-0.07670.1151-0.00550.05090.1066-0.0496-0.04650.2363-0.00570.00020.08350.01410.023315.215911.815333.7397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 102
2X-RAY DIFFRACTION2A103 - 349
3X-RAY DIFFRACTION3B2 - 19
4X-RAY DIFFRACTION4B20 - 348

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