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- PDB-1xwi: Crystal Structure of VPS4B -

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Basic information

Entry
Database: PDB / ID: 1xwi
TitleCrystal Structure of VPS4B
ComponentsSKD1 protein
KeywordsPROTEIN TRANSPORT / VPS4B / SKD1 / AAA ATPase
Function / homology
Function and homology information


protein depolymerization / late endosomal microautophagy / positive regulation of centriole elongation / late endosome to lysosome transport via multivesicular body sorting pathway / negative regulation of exosomal secretion / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / ESCRT III complex disassembly / nuclear membrane reassembly / multivesicular body sorting pathway / vacuole organization ...protein depolymerization / late endosomal microautophagy / positive regulation of centriole elongation / late endosome to lysosome transport via multivesicular body sorting pathway / negative regulation of exosomal secretion / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / ESCRT III complex disassembly / nuclear membrane reassembly / multivesicular body sorting pathway / vacuole organization / regulation of centrosome duplication / midbody abscission / positive regulation of exosomal secretion / membrane fission / plasma membrane repair / multivesicular body assembly / establishment of blood-brain barrier / cholesterol transport / endosome to lysosome transport via multivesicular body sorting pathway / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Flemming body / regulation of mitotic spindle assembly / vesicle-fusing ATPase / endosomal transport / mitotic metaphase chromosome alignment / ATPase complex / response to lipid / nucleus organization / viral budding via host ESCRT complex / canonical Wnt signaling pathway / autophagosome maturation / positive regulation of G2/M transition of mitotic cell cycle / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / macroautophagy / potassium ion transport / Budding and maturation of HIV virion / autophagy / spindle pole / late endosome membrane / protein transport / angiogenesis / midbody / endosome / endosome membrane / centrosome / protein-containing complex binding / protein homodimerization activity / ATP hydrolysis activity / extracellular exosome / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / AAA ATPase, 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 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / Helicase, Ruva Protein; domain 3 / 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
Vacuolar protein sorting-associated protein 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsScott, A. / Sundquist, W.I. / Hill, C.P.
CitationJournal: Embo J. / Year: 2005
Title: Structural and mechanistic studies of VPS4 proteins
Authors: Scott, A. / Chung, H.Y. / Gonciarz-Swiatek, M. / Hill, G.C. / Whitby, F.G. / Gaspar, J. / Holton, J.M. / Viswanathan, R. / Ghaffarian, S. / Hill, C.P. / Sundquist, W.I.
History
DepositionNov 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: SKD1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8753
Polymers35,6831
Non-polymers1922
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.058, 88.058, 112.574
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsCrystal structure is monomeric. Biological function probably requires nucleotide-dependent oligomerization.

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Components

#1: Protein SKD1 protein / Vacuolar sorting protein 4b


Mass: 35682.855 Da / Num. of mol.: 1 / Fragment: residues 123-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS4B, SKD1, VPS42 / Plasmid: modified pET16b / Production host: Escherichia coli (E. coli) / References: UniProt: O75351
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 300 K / pH: 7.5
Details: Ammonium Sulfate, HEPES, NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9798
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2003
RadiationMonochromator: SYNCHROTRON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.8→76.6 Å / Num. obs: 12140 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 47.85 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→2.87 Å / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.285 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.8→76.7 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.144 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.717 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1190 9.8 %RANDOM
Rwork0.192 ---
obs0.199 10917 98.8 %-
all-10917 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.85 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.5 Å20 Å2
2--1 Å20 Å2
3----1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→76.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2508 0 10 9 2527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222406
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.9623255
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.415298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00223.762101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.64115429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4051518
X-RAY DIFFRACTIONr_chiral_restr0.110.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021784
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.21061
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.21648
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9871.51529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68622430
X-RAY DIFFRACTIONr_scbond_it2.2943962
X-RAY DIFFRACTIONr_scangle_it3.8044.5825
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 95 -
Rwork0.303 822 -
obs--100 %

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