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- PDB-4niq: Crystal Structure of Vps4 MIT-Vfa1 MIM2 -

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Basic information

Entry
Database: PDB / ID: 4niq
TitleCrystal Structure of Vps4 MIT-Vfa1 MIM2
Components
  • VPS4-associated protein 1
  • Vacuolar protein sorting-associated protein 4
KeywordsPROTEIN TRANSPORT / cytosol
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 / vacuolar transport / nuclear membrane reassembly ...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 / vacuolar transport / nuclear membrane reassembly / multivesicular body sorting pathway / vacuole organization / midbody abscission / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / endosomal transport / ATPase complex / nucleus organization / ATPase activator activity / 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
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-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 / molecular replacement / Resolution: 2.301 Å
AuthorsVild, C.J. / Xu, Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Vfa1 Binds to the N-terminal Microtubule-interacting and Trafficking (MIT) Domain of Vps4 and Stimulates Its ATPase Activity.
Authors: Vild, C.J. / Xu, Z.
History
DepositionNov 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: VPS4-associated protein 1
B: Vacuolar protein sorting-associated protein 4
D: VPS4-associated protein 1


Theoretical massNumber of molelcules
Total (without water)24,4374
Polymers24,4374
Non-polymers00
Water00
1
A: Vacuolar protein sorting-associated protein 4
C: VPS4-associated protein 1


Theoretical massNumber of molelcules
Total (without water)12,2192
Polymers12,2192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-11 kcal/mol
Surface area6260 Å2
MethodPISA
2
B: Vacuolar protein sorting-associated protein 4
D: VPS4-associated protein 1


Theoretical massNumber of molelcules
Total (without water)12,2192
Polymers12,2192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-11 kcal/mol
Surface area5980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.476, 56.711, 84.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vacuolar protein sorting-associated protein 4 / DOA4-independent degradation protein 6 / Protein END13 / Vacuolar protein-targeting protein 10


Mass: 9527.703 Da / Num. of mol.: 2 / Fragment: MIT domain: unp residues 1-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: Baker's yeast
Gene: CSC1, DID6, END13, GRD13, P9705.10, VPL4, VPS4, VPT10, YPR173C
Plasmid: ppSUMO2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P52917
#2: Protein/peptide VPS4-associated protein 1


Mass: 2690.957 Da / Num. of mol.: 2 / Fragment: MIM2: unp residues 182-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: Baker's yeast / Gene: SYGP-ORF44, VFA1, YER128W / Plasmid: ppSUMO2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P40080

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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: 1.88 Å3/Da / Density % sol: 34.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% PEG 4000, 10% (v/v) isopropanol, 0.1M HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9998 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2013
RadiationMonochromator: diamond laue monochromators with beryllium lenses
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 8671 / Num. obs: 8662 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 43.11 Å2 / Rmerge(I) obs: 0.044 / Χ2: 0.903 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.387.30.3368400.891100
2.38-2.487.20.2478500.9421100
2.48-2.597.30.1898531.0331100
2.59-2.737.30.1338491.0511100
2.73-2.97.30.1048400.9191100
2.9-3.127.20.0678590.8391100
3.12-3.447.20.0558630.971100
3.44-3.937.10.0428691.1271100
3.93-4.9570.0278940.6511100
4.95-506.40.0239450.594198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å35 Å
Translation2.5 Å35 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.301→34.998 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.36 / Phase error: 28.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 861 10 %
Rwork0.2358 --
obs0.2379 8613 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.25 Å2 / Biso mean: 48.6229 Å2 / Biso min: 24.76 Å2
Refinement stepCycle: LAST / Resolution: 2.301→34.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1597 0 0 0 1597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111624
X-RAY DIFFRACTIONf_angle_d1.3992197
X-RAY DIFFRACTIONf_chiral_restr0.075248
X-RAY DIFFRACTIONf_plane_restr0.005284
X-RAY DIFFRACTIONf_dihedral_angle_d18.037596
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3013-2.44550.34281410.301312691410100
2.4455-2.63430.33471390.274412581397100
2.6343-2.89920.3161410.299312711412100
2.8992-3.31850.26611430.244512811424100
3.3185-4.17980.27061450.234913041449100
4.1798-35.00180.20081520.19871369152199

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