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- PDB-9bl8: MIT (L7C/A43C) Domain of Vps4p -

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Basic information

Entry
Database: PDB / ID: 9bl8
TitleMIT (L7C/A43C) Domain of Vps4p
ComponentsVacuolar protein sorting-associated protein 4
KeywordsPROTEIN TRANSPORT / Vps4 ESCRT ESCRTIII MIT MIM Disulfide Bond
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 / multivesicular body sorting pathway ...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 / 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 / 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 / AAA ATPase, AAA+ lid domain / 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 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
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: 1.3 Å
AuthorsWienkers, H.J. / Han, H. / Whitby, F.G. / Hill, C.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biorxiv / Year: 2024
Title: Vps4 substrate binding and coupled mechanisms of Vps4p substrate recruitment and release from autoinhibition.
Authors: Wienkers, H.J. / Han, H. / Whitby, F.G. / Hill, C.P.
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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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)9,5552
Polymers9,5201
Non-polymers351
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)20.699, 42.939, 96.463
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 9519.728 Da / Num. of mol.: 1 / Fragment: MIT Domain / Mutation: L7C, A43C
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
Production host: Escherichia coli (E. coli) / References: UniProt: P52917
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Vps4 MIT Domain (10mg/ml) in 20mM Tris pH = 8, 100mM NaCl mixed in a 1:2 ratio with 0.2M Calcium Chloride dihydrate, 0.1M sodium acetate trihydrate pH=4.6, 20% 2-propanol
PH range: 4.6-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.3→32.07 Å / Num. obs: 19914 / % possible obs: 90.05 % / Redundancy: 3.9 % / Biso Wilson estimate: 10.9 Å2 / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.1327 / Rpim(I) all: 0.06755 / Rrim(I) all: 0.15 / Net I/σ(I): 7.95
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.4811 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 1397 / CC1/2: 0.734 / Rpim(I) all: 0.2675 / Rrim(I) all: 0.5555 / % possible all: 92.59

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→32.07 Å / SU ML: 0.1205 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 15.616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1803 1992 10.01 %
Rwork0.136 17918 -
obs0.1405 19910 90.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.48 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms666 0 1 150 817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065739
X-RAY DIFFRACTIONf_angle_d0.84721009
X-RAY DIFFRACTIONf_chiral_restr0.064111
X-RAY DIFFRACTIONf_plane_restr0.0052131
X-RAY DIFFRACTIONf_dihedral_angle_d15.2347300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.24361400.19321259X-RAY DIFFRACTION92.59
1.33-1.370.23761430.16591280X-RAY DIFFRACTION90.81
1.37-1.410.21871440.16661302X-RAY DIFFRACTION93.96
1.41-1.450.23981460.17381315X-RAY DIFFRACTION94.08
1.45-1.50.18131430.13051288X-RAY DIFFRACTION92.14
1.5-1.560.17041470.12191317X-RAY DIFFRACTION94.88
1.56-1.640.17741440.11471299X-RAY DIFFRACTION91.91
1.64-1.720.18551480.13051328X-RAY DIFFRACTION92.77
1.72-1.830.20411430.12951285X-RAY DIFFRACTION91.83
1.83-1.970.151370.12471238X-RAY DIFFRACTION87.64
1.97-2.170.17541410.11421267X-RAY DIFFRACTION89
2.17-2.480.13861420.11721281X-RAY DIFFRACTION88.44
2.48-3.130.17221390.13671258X-RAY DIFFRACTION85.6
3.13-32.070.1911350.15531201X-RAY DIFFRACTION77.14

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