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- PDB-7l9x: Structure of VPS4B in complex with an allele-specific covalent in... -

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Basic information

Entry
Database: PDB / ID: 7l9x
TitleStructure of VPS4B in complex with an allele-specific covalent inhibitor
ComponentsVacuolar protein sorting-associated protein 4BVacuole
KeywordsPROTEIN TRANSPORT / chemical Inhibitor / hydrolase / ATPase / AAA superfamily
Function / homology
Function and homology information


protein depolymerization / positive regulation of centriole elongation / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / negative regulation of exosomal secretion / late endosome to lysosome transport via multivesicular body sorting pathway / ESCRT III complex disassembly / late endosomal microautophagy / regulation of centrosome duplication / nuclear membrane reassembly / midbody abscission ...protein depolymerization / positive regulation of centriole elongation / ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway / negative regulation of exosomal secretion / late endosome to lysosome transport via multivesicular body sorting pathway / ESCRT III complex disassembly / late endosomal microautophagy / regulation of centrosome duplication / nuclear membrane reassembly / midbody abscission / establishment of blood-brain barrier / multivesicular body sorting pathway / vacuole organization / membrane fission / plasma membrane repair / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / endosome to lysosome transport via multivesicular body sorting pathway / cholesterol transport / regulation of mitotic spindle assembly / vesicle-fusing ATPase / Flemming body / endosomal transport / mitotic metaphase chromosome alignment / response to lipid / ATPase complex / nucleus organization / viral budding via host ESCRT complex / autophagosome maturation / canonical Wnt signaling pathway / nuclear pore / Endosomal Sorting Complex Required For Transport (ESCRT) / positive regulation of G2/M transition of mitotic cell cycle / viral budding from plasma membrane / macroautophagy / Budding and maturation of HIV virion / potassium ion transport / autophagy / spindle pole / protein transport / late endosome membrane / midbody / angiogenesis / endosome membrane / endosome / centrosome / protein-containing complex binding / protein homodimerization activity / ATP hydrolysis activity / extracellular exosome / 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 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site ...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
Chem-XQV / Vacuolar protein sorting-associated protein 4B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsGrasso, M. / Cupido, T. / Kapoor, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 T32 CA 9673-40 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2021
Title: A chemical genetics approach to examine the functions of AAA proteins.
Authors: Cupido, T. / Jones, N.H. / Grasso, M.J. / Pisa, R. / Kapoor, T.M.
History
DepositionJan 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,0403
Polymers49,5861
Non-polymers4532
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.876, 77.876, 132.826
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65

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Components

#1: Protein Vacuolar protein sorting-associated protein 4B / Vacuole / Cell migration-inducing gene 1 protein / Suppressor of K(+) transport growth defect 1 / Protein SKD1


Mass: 49586.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS4B, SKD1, VPS42, MIG1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75351, vesicle-fusing ATPase
#2: Chemical ChemComp-XQV / N-{3-[(8-phenyl[1,2,4]triazolo[1,5-a]pyridin-2-yl)amino]phenyl}propanamide


Mass: 357.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM NH4SO4, 100 mM Hepes pH 7.5, 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.81→29.24 Å / Num. obs: 11046 / % possible obs: 98.72 % / Redundancy: 2 % / Biso Wilson estimate: 94.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02234 / Net I/σ(I): 14.62
Reflection shellResolution: 2.81→2.87 Å / Rmerge(I) obs: 0.3546 / Num. unique obs: 1047 / CC1/2: 0.84 / Χ2: 1.19

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Cootmodel building
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XWI
Resolution: 2.81→29.24 Å / SU ML: 0.4794 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.8585
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2669 1106 10.07 %
Rwork0.2092 9873 -
obs0.2149 10979 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.66 Å2
Refinement stepCycle: LAST / Resolution: 2.81→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2254 0 32 33 2319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372342
X-RAY DIFFRACTIONf_angle_d0.71673183
X-RAY DIFFRACTIONf_chiral_restr0.0431364
X-RAY DIFFRACTIONf_plane_restr0.0047410
X-RAY DIFFRACTIONf_dihedral_angle_d8.85061932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.940.4671270.41181112X-RAY DIFFRACTION90.9
2.94-3.10.36341420.30411267X-RAY DIFFRACTION99.93
3.1-3.290.34021370.27751230X-RAY DIFFRACTION99.93
3.29-3.540.32651410.26351255X-RAY DIFFRACTION100
3.54-3.90.32541420.22711245X-RAY DIFFRACTION99.78
3.9-4.460.25411340.19491246X-RAY DIFFRACTION100
4.46-5.610.23371400.19311257X-RAY DIFFRACTION100
5.61-29.240.2221430.17191261X-RAY DIFFRACTION99.93

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