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- PDB-5fvk: Crystal structure of Vps4-Vfa1 complex from S.cerevisiae at 1.66 ... -

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Basic information

Entry
Database: PDB / ID: 5fvk
TitleCrystal structure of Vps4-Vfa1 complex from S.cerevisiae at 1.66 A resolution.
Components
  • VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4Vacuole
  • VPS4-ASSOCIATED PROTEIN 1
KeywordsHYDROLASE / VPS4 / VFA1 / MIT DOMAIN / YEAST / ATPASE
Function / homology
Function and homology information


ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / vacuolar transport / sterol metabolic process / nuclear membrane reassembly / midbody abscission ...ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / vacuolar transport / sterol metabolic process / nuclear membrane reassembly / midbody abscission / vacuole organization / multivesicular body sorting pathway / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / nucleus organization / endosomal transport / ATPase complex / ATPase activator activity / autophagosome maturation / nuclear pore / macroautophagy / autophagy / protein transport / midbody / endosome / endoplasmic reticulum / ATP hydrolysis activity / protein homodimerization activity / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
VPS4-associated protein 1 / AAA-ATPase Vps4-associated protein 1 / Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / 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 ...VPS4-associated protein 1 / AAA-ATPase Vps4-associated protein 1 / Vacuolar protein sorting-associated protein 4, MIT domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / 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 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
VPS4-associated protein 1 / Vacuolar protein sorting-associated protein 4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.658 Å
AuthorsKojima, R. / Obita, T. / Onoue, K. / Mizuguchi, M.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Fine-Tuning of Mit Interacting Motif 2 (Mim2) and Allosteric Regulation of Escrt-III by Vps4 in Yeast.
Authors: Kojima, R. / Obita, T. / Onoue, K. / Mizuguchi, M.
History
DepositionFeb 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
C: VPS4-ASSOCIATED PROTEIN 1
D: VPS4-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)24,0894
Polymers24,0894
Non-polymers00
Water1,928107
1
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
C: VPS4-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)12,0452
Polymers12,0452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-14.3 kcal/mol
Surface area6380 Å2
MethodPISA
2
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
D: VPS4-ASSOCIATED PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)12,0452
Polymers12,0452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-12.2 kcal/mol
Surface area6400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.830, 56.460, 84.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4 / Vacuole / DOA4-INDEPENDENT DEGRADATION PROTEIN 6 / PROTEIN END13 / VACUOLAR PROTEIN-TARGETING PROTEIN 10 / VPS4


Mass: 9440.625 Da / Num. of mol.: 2 / Fragment: MIT DOMAIN, RESIDUES 1-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P52917, vesicle-fusing ATPase
#2: Protein/peptide VPS4-ASSOCIATED PROTEIN 1 / VFA1


Mass: 2603.879 Da / Num. of mol.: 2 / Fragment: RESIDUES 182-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P40080
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.92 Å3/Da / Density % sol: 35.83 % / Description: NONE
Crystal growpH: 4 / Details: pH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→31.99 Å / Num. obs: 22657 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.4 % / Biso Wilson estimate: 19.62 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.1
Reflection shellResolution: 1.66→1.75 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V6X

2v6x


Resolution: 1.658→31.994 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 1157 5.1 %
Rwork0.1837 --
obs0.1857 22604 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.658→31.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1657 0 0 107 1764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061712
X-RAY DIFFRACTIONf_angle_d0.9382315
X-RAY DIFFRACTIONf_dihedral_angle_d15.209659
X-RAY DIFFRACTIONf_chiral_restr0.041255
X-RAY DIFFRACTIONf_plane_restr0.004298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.658-1.73350.26971280.22642625X-RAY DIFFRACTION100
1.7335-1.82490.24071520.20862642X-RAY DIFFRACTION100
1.8249-1.93920.26111420.19992656X-RAY DIFFRACTION100
1.9392-2.08890.23841520.192646X-RAY DIFFRACTION100
2.0889-2.2990.22081500.18052651X-RAY DIFFRACTION100
2.299-2.63160.25611340.19142694X-RAY DIFFRACTION100
2.6316-3.3150.22391560.18872713X-RAY DIFFRACTION100
3.315-31.99990.19131430.16552820X-RAY DIFFRACTION99
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)
13.4765-1.11911.52582.4926-0.22292.3376-0.3636-0.48870.47850.39320.2501-0.3494-0.1783-0.12460.05510.17530.0275-0.05950.1457-0.05950.137618.2832.751313.3073
26.4451-4.65691.81886.4822-2.01821.81850.12910.357-0.0309-0.1054-0.1816-0.3324-0.01940.13780.02250.095-0.01210.00470.0938-0.02590.07422.202124.35756.2597
33.83113.5739-0.04454.1687-1.68693.4269-0.2659-0.30351.31560.445-0.17960.1889-0.4912-0.07050.35140.31080.1335-0.04550.2498-0.02270.49652.392241.85867.0684
44.8597-0.02720.54891.53071.87432.3797-0.3640.32841.6002-0.06720.607-0.4322-1.5205-0.1279-0.20120.6634-0.0737-0.15190.21480.09030.510613.058746.15612.0787
53.9926-0.34782.385.9431-0.79965.0363-0.16150.01150.1239-0.4155-0.179-0.4644-0.26820.45390.30280.2057-0.03210.03630.1740.03930.398823.812636.40064.7771
65.482-4.1310.92334.5897-4.25728.73090.41350.11821.22370.3173-0.50820.7405-0.5616-0.0490.23540.3934-0.03090.06230.3137-0.10550.48365.221133.9686-24.5377
77.32192.9388-3.41383.8114-1.75234.024-0.01850.36150.5576-0.01230.33170.7416-0.4399-0.4536-0.13920.13280.034-0.01150.19520.05030.157-2.626927.4264-12.3642
82.47320.8316-0.78433.4969-0.95552.4982-0.04970.3785-0.2555-0.17960.1031-0.01530.05010.0257-0.03690.13960.0008-0.00210.1573-0.01030.05565.571822.6982-14.9758
97.41465.8757-1.08817.3964-0.64411.59390.2559-0.2172-0.11190.3987-0.20830.1240.052-0.00960.0080.12650.0250.01090.09340.0050.06652.565917.2245-6.2973
104.3194-4.9184-4.59069.41027.85546.78880.15520.56230.7351-0.18080.0175-0.3362-0.65590.1809-0.14130.2751-0.13760.10530.35030.02630.420619.651134.3035-15.5901
117.38812.06650.24912.01481.2131.6640.4523-0.33011.0632-0.15370.1037-0.4356-0.30230.1183-0.08890.3986-0.27870.18750.1636-0.22820.470313.330639.3873-8.0504
125.75172.8373-2.03118.0768-2.78045.17580.1685-0.17990.08530.2303-0.08590.0316-0.43430.15030.0040.2297-0.02220.07690.1384-0.02230.18012.860230.7811-6.0117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 49 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 50 THROUGH 82 )
3X-RAY DIFFRACTION3CHAIN 'C' AND (RESID 183 THROUGH 188 )
4X-RAY DIFFRACTION4CHAIN 'C' AND (RESID 189 THROUGH 195 )
5X-RAY DIFFRACTION5CHAIN 'C' AND (RESID 196 THROUGH 203 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 1 THROUGH 5 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 6 THROUGH 25 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 26 THROUGH 49 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 50 THROUGH 82 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 184 THROUGH 188 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 189 THROUGH 195 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 196 THROUGH 202 )

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