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- PDB-6p13: Structure of spastin AAA domain (T692A mutant) in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 6p13
TitleStructure of spastin AAA domain (T692A mutant) in complex with a diaminotriazole-based inhibitor (crystal form A)
ComponentsSpastin
KeywordsISOMERASE/ISOMERASE INHIBITOR / inhibitor / complex / AAA protein / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of synaptic assembly at neuromuscular junction / hemocyte migration / positive regulation of axon extension involved in regeneration / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of neuromuscular synaptic transmission / positive regulation of neuromuscular synaptic transmission / positive regulation of synaptic assembly at neuromuscular junction / microtubule-severing ATPase / microtubule severing ATPase activity / regulation of terminal button organization ...negative regulation of synaptic assembly at neuromuscular junction / hemocyte migration / positive regulation of axon extension involved in regeneration / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of neuromuscular synaptic transmission / positive regulation of neuromuscular synaptic transmission / positive regulation of synaptic assembly at neuromuscular junction / microtubule-severing ATPase / microtubule severing ATPase activity / regulation of terminal button organization / mitotic chromosome movement towards spindle pole / microtubule severing / positive regulation of lipid metabolic process / positive regulation of microtubule depolymerization / mitotic spindle elongation / negative regulation of microtubule depolymerization / positive regulation of dendrite morphogenesis / protein hexamerization / mitotic sister chromatid segregation / alpha-tubulin binding / lipid droplet / adult locomotory behavior / neuromuscular junction / locomotory behavior / microtubule cytoskeleton organization / spindle / terminal bouton / nervous system development / chromosome / microtubule cytoskeleton / microtubule binding / microtubule / cell division / centrosome / ATP hydrolysis activity / ATP binding / membrane / cytoplasm
Similarity search - Function
Spastin / 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 / ATPase, AAA-type, conserved site ...Spastin / 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 / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / 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
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPisa, R. / Cupido, T. / Kapoor, T.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM98579 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM130234-01 United States
CitationJournal: Cell Chem Biol / Year: 2019
Title: Analyzing Resistance to Design Selective Chemical Inhibitors for AAA Proteins.
Authors: Pisa, R. / Cupido, T. / Steinman, J.B. / Jones, N.H. / Kapoor, T.M.
History
DepositionMay 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
B: Spastin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8904
Polymers34,2911
Non-polymers5993
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, differential scanning fluorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-28 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.698, 79.698, 96.873
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Spastin / D-Spastin / Dm-Spastin / Dspastin


Mass: 34291.004 Da / Num. of mol.: 1 / Fragment: AAA domain (UNP residues 445-758) / Mutation: T692A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: spas, CG5977 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I0P1, microtubule-severing ATPase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NKY / 3-{[5-amino-1-(2-fluoro-6-methoxybenzene-1-carbonyl)-1H-1,2,4-triazol-3-yl]amino}-N-methylbenzamide


Mass: 384.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17FN6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, pH 5.0-6.5, 2% PEG4000, 15% MPD
PH range: 5.0-6.5

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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: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2018
Diffraction measurementDetails: 1.00 degrees, 0.20 sec, detector distance 220.00 mm
Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionAv R equivalents: 0.052 / Number: 400597
ReflectionResolution: 2.1→50 Å / Num. obs: 20423 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 46.0316109984 Å2 / Rmerge(I) obs: 0.043 / Net I/av σ(I): 42 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1015 / CC1/2: 0.869 / % possible all: 100
Cell measurementReflection used: 400597

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3B9P

3b9p


Resolution: 2.1→39.849 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.06
RfactorNum. reflection% reflection
Rfree0.2454 2048 10.04 %
Rwork0.2067 --
obs0.2106 20389 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.79 Å2 / Biso mean: 50.7305 Å2 / Biso min: 27.48 Å2
Refinement stepCycle: final / Resolution: 2.1→39.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 41 108 2189
Biso mean--45.94 55.78 -
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032129
X-RAY DIFFRACTIONf_angle_d0.4872905
X-RAY DIFFRACTIONf_chiral_restr0.039352
X-RAY DIFFRACTIONf_plane_restr0.003375
X-RAY DIFFRACTIONf_dihedral_angle_d10.1131716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.14890.31631390.26281216100
2.1489-2.20260.33351320.27521221100
2.2026-2.26210.31491310.25321223100
2.2621-2.32870.32021360.25941222100
2.3287-2.40390.31091390.2551216100
2.4039-2.48980.30481370.24791235100
2.4898-2.58940.27591350.24021204100
2.5894-2.70730.27981420.25431216100
2.7073-2.850.29791370.24211227100
2.85-3.02850.27811350.23751206100
3.0285-3.26220.25831370.2311233100
3.2622-3.59030.2281370.20661229100
3.5903-4.10930.24011370.17861219100
4.1093-5.17560.19331370.1681236100
5.1756-39.8490.21621370.1869123898

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