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- PDB-5fvl: Crystal structure of Vps4-Vps20 complex from S.cerevisiae -

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Basic information

Entry
Database: PDB / ID: 5fvl
TitleCrystal structure of Vps4-Vps20 complex from S.cerevisiae
Components
  • VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 20
  • VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
KeywordsVIRAL PROTEIN / MIT DOMAIN / ATPASE / YEAST
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 / Macroautophagy / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process ...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 / Macroautophagy / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / ESCRT III complex / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / ATP export / nuclear membrane reassembly / multivesicular body sorting pathway / vacuole organization / midbody abscission / membrane fission / plasma membrane repair / vesicle budding from membrane / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / reticulophagy / vacuolar membrane / endosomal transport / ATPase complex / nucleus organization / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein transport / midbody / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Snf7 family ...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 / Snf7 family / Snf7 / 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
Vacuolar protein sorting-associated protein 4 / Vacuolar protein sorting-associated protein 20
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.973 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 1.2Jan 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

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Assembly

Deposited unit
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 20
D: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 20


Theoretical massNumber of molelcules
Total (without water)24,9324
Polymers24,9324
Non-polymers00
Water45025
1
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
D: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 20


Theoretical massNumber of molelcules
Total (without water)12,4662
Polymers12,4662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-9.8 kcal/mol
Surface area7290 Å2
MethodPISA
2
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4
C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 20


Theoretical massNumber of molelcules
Total (without water)12,4662
Polymers12,4662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-9.5 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.140, 53.890, 70.170
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 / VPS4 / DOA4-INDEPENDENT DEGRADATION PROTEIN 6 / PROTEIN END13 / VACUOLAR PROTEIN-TARGETING PROTEIN 10


Mass: 9578.771 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
#2: Protein/peptide VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 20 / VPS20 / AMINO ACID SENSOR-INDEPENDENT PROTEIN 10 / CHARGED MULTIVESICULAR BODY PROTEIN 6 / ESCRT- ...VPS20 / AMINO ACID SENSOR-INDEPENDENT PROTEIN 10 / CHARGED MULTIVESICULAR BODY PROTEIN 6 / ESCRT-III COMPLEX SUBUNIT VPS20 / VACUOLAR PROTEIN-TARGETING PROTEIN 20


Mass: 2887.267 Da / Num. of mol.: 2 / Fragment: RESIDUES 170-195
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: Q04272
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.83 Å3/Da / Density % sol: 32.62 % / Description: NONE
Crystal growpH: 8.6 / Details: pH 8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1
DetectorDetector: CCD / Date: Dec 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→39.7 Å / Num. obs: 13410 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.3 % / Biso Wilson estimate: 16.94 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 15
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 6.1 / % 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: 1.973→39.696 Å / SU ML: 0.19 / σ(F): 1.38 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 659 4.9 %
Rwork0.1833 --
obs0.1858 13369 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.973→39.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 0 25 1701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071716
X-RAY DIFFRACTIONf_angle_d0.9422313
X-RAY DIFFRACTIONf_dihedral_angle_d15.527667
X-RAY DIFFRACTIONf_chiral_restr0.042253
X-RAY DIFFRACTIONf_plane_restr0.004301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9733-2.12560.24291330.18932488X-RAY DIFFRACTION100
2.1256-2.33950.23841180.17872519X-RAY DIFFRACTION100
2.3395-2.6780.24511350.18632508X-RAY DIFFRACTION100
2.678-3.37370.22441410.18862520X-RAY DIFFRACTION100
3.3737-39.70430.22811320.17882675X-RAY DIFFRACTION100

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