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- PDB-3eie: Crystal Structure of S.cerevisiae Vps4 in the SO4-bound state -

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Basic information

Entry
Database: PDB / ID: 3eie
TitleCrystal Structure of S.cerevisiae Vps4 in the SO4-bound state
ComponentsVacuolar protein sorting-associated protein 4
KeywordsPROTEIN TRANSPORT / AAA ATPase / ATP-binding cassette / ATP-binding / Endosome / Membrane / Nucleotide-binding / Phosphoprotein / Transport
Function / homology
Function and homology information


ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission ...ESCRT IV complex / Sealing of the nuclear envelope (NE) by ESCRT-III / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / multivesicular body sorting pathway / vacuole organization / plasma membrane repair / membrane fission / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / endosomal transport / nucleus organization / ATPase complex / autophagosome maturation / nuclear pore / macroautophagy / autophagy / protein transport / midbody / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Vacuolar protein sorting-associated protein 4, MIT domain / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain ...Vacuolar protein sorting-associated protein 4, MIT domain / MIT (microtubule interacting and transport) domain / MIT domain superfamily / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGonciarz, M.D. / Whitby, F.G. / Eckert, D.M. / Kieffer, C. / Heroux, A. / Sundquist, W.I. / Hill, C.P.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Biochemical and structural studies of yeast vps4 oligomerization.
Authors: Gonciarz, M.D. / Whitby, F.G. / Eckert, D.M. / Kieffer, C. / Heroux, A. / Sundquist, W.I. / Hill, C.P.
History
DepositionSep 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7243
Polymers35,5321
Non-polymers1922
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.830, 110.830, 169.120
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 4 / Protein END13 / DOA4-independent degradation protein 6 / Vacuolar protein-targeting protein 10


Mass: 35532.188 Da / Num. of mol.: 1 / Fragment: UNP residues 122-437 / Mutation: E233Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10
Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P52917
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 4.18 Å3/Da / Density % sol: 70.55 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.6M Ammonium sulfate, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2005
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→33 Å / Num. obs: 17628 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.109 / Rsym value: 0.098
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.4.0054refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→33 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.893 / SU B: 23.157 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28701 1152 6.8 %RANDOM
Rwork0.241 ---
all0.24402 ---
obs0.24402 15893 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0.38 Å20 Å2
2---0.76 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 10 35 2396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222399
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9843244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3475300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17624.64699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98415437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6951515
X-RAY DIFFRACTIONr_chiral_restr0.1050.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211759
X-RAY DIFFRACTIONr_mcbond_it0.5831.51508
X-RAY DIFFRACTIONr_mcangle_it1.10522441
X-RAY DIFFRACTIONr_scbond_it1.4133891
X-RAY DIFFRACTIONr_scangle_it2.5094.5803
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 78 -
Rwork0.345 1152 -
obs--98.09 %
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)
12.13610.38261.00094.26480.31653.2486-0.09940.06330.0654-0.14670.0626-0.3492-0.19440.29710.03680.2935-0.02080.03680.20540.00740.244835.730511.43779.3823
22.63-1.39720.06353.0697-1.00781.33710.1395-0.0337-0.2017-0.1747-0.0415-0.2810.24620.3238-0.09810.3326-0.0882-0.06180.2710.00120.320836.8633.628117.3038
32.37152.1261-0.00654.50670.28953.55280.10740.13610.0926-0.00530.0145-0.0923-0.11170.1874-0.12180.3175-0.0241-0.02640.20440.02050.285229.68888.48977.6642
41.9860.28270.60518.52271.29680.35710.04430.11320.358-0.375-0.13980.7543-0.2432-0.57930.09550.4198-0.00460.01260.4357-0.0010.43339.59215.172711.3399
56.0413-1.1138-1.10181.77060.99641.26830.07360.2234-0.3321-0.0325-0.04490.37280.0858-0.2876-0.02860.3313-0.02010.0020.28410.01480.310619.6014-3.32219.2641
64.8457-2.5468-2.58764.57654.0098.1419-0.0791-0.2731-0.02610.4286-0.13810.31470.3008-0.17310.21720.3111-0.0499-0.00280.21730.02740.303425.02714.17211.6417
72.0574-1.0867-2.51860.90021.05113.3219-0.7144-0.89710.18480.93140.28671.1999-0.0383-1.33470.42770.5092-0.13720.08110.35160.05370.59199.54993.601221.7657
86.3511-5.82350.70887.053-2.28496.3264-0.2267-1.1035-0.05750.29290.11730.3828-0.1899-0.0960.10950.3243-0.08450.02190.23340.05080.271418.6054-2.536219.931
910.5136-13.5659-1.602417.50442.06760.2442-0.2507-0.4312-1.6882-0.1786-0.8531.77310.9211.86371.10380.738-0.19350.16470.72620.0350.820229.0043-8.926517.1808
106.99334.71041.10567.677-4.97417.43560.3006-0.2395-0.5873-0.4609-0.3132-0.44630.04730.47890.01260.2584-0.0596-0.06410.24590.00840.298728.97613.453514.6424
114.50573.12440.13694.4182-2.58085.20480.1579-0.7132-0.24940.4587-0.23430.23010.2272-0.23890.07650.4535-0.14170.06140.2545-0.06540.213525.07389.305625.2658
120.0955-0.31880.33582.7352-1.31931.2040.0034-0.2612-0.07140.1491-0.07360.00660.01170.24390.07010.2829-0.0726-0.010.2078-0.01560.330535.504227.931613.9762
133.3633.85272.87066.19051.95723.4479-0.10330.3092-0.0664-0.2080.2898-0.1875-0.01990.3179-0.18650.2989-0.0692-0.0240.257-0.05560.344637.715835.15541.4939
144.5240.5429-0.41214.6352-0.6732.26960.0289-0.1409-0.02150.21670.01570.14290.1282-0.0864-0.04470.309-0.0787-0.01230.1649-0.05230.365530.829234.103610.6019
157.7219-1.41884.56210.8040.61096.5602-0.2096-0.3916-0.29550.15130.4050.6164-0.2983-0.7555-0.19540.3979-0.0764-0.11720.2262-0.09980.375823.683742.2825-3.7678
161.96270.98630.68742.5285-0.51323.6259-0.02370.42220.605-0.17560.11380.0107-0.16170.1478-0.09010.577-0.0085-0.05540.38260.00160.49526.428154.0821-10.9103
176.96912.27290.86931.6213-0.68841.18820.1810.08170.573-0.69060.2114-0.8405-1.19530.582-0.39240.5104-0.0677-0.07760.35780.05310.485529.714154.305-12.8007
184.93580.33151.68950.2812-0.06910.70710.00460.19220.3453-0.49650.2015-0.1799-0.56280.3194-0.20610.513-0.006-0.0470.4360.04830.489423.047250.3555-16.222
193.7539-0.45992.5145.4094-2.46698.1198-0.16580.17480.39850.33810.11450.3081-0.7663-0.27950.05130.3486-0.073-0.07880.1285-0.07990.429529.004542.26594.4785
201.74060.7746-0.84995.8509-5.06634.4065-0.0063-0.92460.80941.41840.0598-0.3097-0.2699-0.9452-0.05350.7003-0.0978-0.02680.2855-0.2070.134826.818721.742428.5145
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A121 - 151
2X-RAY DIFFRACTION2A152 - 180
3X-RAY DIFFRACTION3A181 - 200
4X-RAY DIFFRACTION4A201 - 211
5X-RAY DIFFRACTION5A212 - 222
6X-RAY DIFFRACTION6A223 - 236
7X-RAY DIFFRACTION7A237 - 252
8X-RAY DIFFRACTION8A253 - 260
9X-RAY DIFFRACTION9A261 - 268
10X-RAY DIFFRACTION10A269 - 275
11X-RAY DIFFRACTION11A276 - 295
12X-RAY DIFFRACTION12A296 - 308
13X-RAY DIFFRACTION13A309 - 323
14X-RAY DIFFRACTION14A324 - 346
15X-RAY DIFFRACTION15A347 - 355
16X-RAY DIFFRACTION16A356 - 364
17X-RAY DIFFRACTION17A369 - 381
18X-RAY DIFFRACTION18A382 - 396
19X-RAY DIFFRACTION19A397 - 414
20X-RAY DIFFRACTION20A415 - 433

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