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- PDB-2zan: Crystal structure of mouse SKD1/VPS4B ATP-form -

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Basic information

Entry
Database: PDB / ID: 2zan
TitleCrystal structure of mouse SKD1/VPS4B ATP-form
ComponentsVacuolar protein sorting-associating protein 4B
KeywordsPROTEIN TRANSPORT / SKD1 / VPS4B / AAA ATPASE / ATP-binding / Membrane / Nucleotide-binding / Phosphorylation / Transport
Function / homology
Function and homology information


protein depolymerization / late endosomal microautophagy / positive regulation of centriole elongation / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to lysosome transport via multivesicular body sorting pathway / negative regulation of exosomal secretion / : / ESCRT III complex disassembly / establishment of blood-brain barrier / vacuolar transport ...protein depolymerization / late endosomal microautophagy / positive regulation of centriole elongation / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to lysosome transport via multivesicular body sorting pathway / negative regulation of exosomal secretion / : / ESCRT III complex disassembly / establishment of blood-brain barrier / vacuolar transport / nuclear membrane reassembly / cholesterol transport / vacuole organization / multivesicular body sorting pathway / midbody abscission / positive regulation of exosomal secretion / membrane fission / multivesicular body assembly / plasma membrane repair / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / endosome organization / regulation of centrosome duplication / endosome to lysosome transport via multivesicular body sorting pathway / Flemming body / regulation of mitotic spindle assembly / nucleus organization / vesicle-fusing ATPase / endosomal transport / viral budding via host ESCRT complex / response to lipid / canonical Wnt signaling pathway / autophagosome maturation / positive regulation of G2/M transition of mitotic cell cycle / mitotic metaphase chromosome alignment / potassium ion transport / viral budding from plasma membrane / central nervous system development / autophagy / spindle pole / late endosome membrane / protein transport / angiogenesis / midbody / endosome / endosome membrane / centrosome / protein-containing complex binding / protein homodimerization activity / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / 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 / Helicase, Ruva Protein; domain 3 ...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 / Helicase, Ruva Protein; domain 3 / 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 / 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
ADENOSINE-5'-TRIPHOSPHATE / Vacuolar protein sorting-associated protein 4B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsInoue, M. / Kawasaki, M. / Kamikubo, H. / Kataoka, M. / Kato, R. / Yoshimori, T. / Wakatsuki, S.
CitationJournal: Traffic / Year: 2008
Title: Nucleotide-dependent conformational changes and assembly of the AAA ATPase SKD1/VPS4B
Authors: Inoue, M. / Kamikubo, H. / Kataoka, M. / Kato, R. / Yoshimori, T. / Wakatsuki, S. / Kawasaki, M.
History
DepositionOct 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associating protein 4B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0203
Polymers49,4881
Non-polymers5312
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.607, 75.607, 131.678
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Vacuolar protein sorting-associating protein 4B / Protein SKD1 / Suppressor of K+ / transport growth defect 1


Mass: 49488.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SKD1 / Plasmid: pProExHTb / Production host: Escherichia coli (E. coli) / References: UniProt: P46467
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5% PEG3350, 0.1 mM MES, ATP soating, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 8611 / % possible obs: 96.5 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.7
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.1 / % possible all: 73.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XWI

1xwi


Resolution: 3→36.46 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.262 345 RANDOM
Rwork0.224 --
all-8571 -
obs-6924 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.83 Å2-17.02 Å20 Å2
2---12.83 Å20 Å2
3---25.65 Å2
Refinement stepCycle: LAST / Resolution: 3→36.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 32 5 2466

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