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- PDB-6nyv: Structure of spastin AAA domain in complex with a quinazoline-bas... -

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Basic information

Entry
Database: PDB / ID: 6nyv
TitleStructure of spastin AAA domain in complex with a quinazoline-based inhibitor
ComponentsSpastin
KeywordsISOMERASE/INHIBITOR / AAA+ protein / ATPase / hydrolase / ENZYME-INHIBITOR complex / ISOMERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of axon extension involved in regeneration / hemocyte migration / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of synaptic assembly at neuromuscular junction / negative regulation of neuromuscular synaptic transmission / positive regulation of neuromuscular synaptic transmission / microtubule-severing ATPase / positive regulation of synaptic assembly at neuromuscular junction / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole ...positive regulation of axon extension involved in regeneration / hemocyte migration / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of synaptic assembly at neuromuscular junction / negative regulation of neuromuscular synaptic transmission / positive regulation of neuromuscular synaptic transmission / microtubule-severing ATPase / positive regulation of synaptic assembly at neuromuscular junction / microtubule severing ATPase activity / mitotic chromosome movement towards spindle pole / microtubule severing / regulation of terminal button organization / positive regulation of lipid metabolic process / mitotic spindle elongation / positive regulation of microtubule depolymerization / negative regulation of microtubule depolymerization / protein hexamerization / positive regulation of dendrite morphogenesis / mitotic sister chromatid segregation / alpha-tubulin binding / lipid droplet / adult locomotory behavior / isomerase activity / locomotory behavior / neuromuscular junction / terminal bouton / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / chromosome / nervous system development / 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 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. ...Spastin / 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
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.425 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: J. Am. Chem. Soc. / Year: 2019
Title: Designing Allele-Specific Inhibitors of Spastin, a Microtubule-Severing AAA Protein.
Authors: Pisa, R. / Cupido, T. / Kapoor, T.M.
History
DepositionFeb 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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)34,9014
Polymers34,3211
Non-polymers5803
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.158, 79.158, 97.076
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: 34321.027 Da / Num. of mol.: 1
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-LBD / N-(3-tert-butyl-1H-pyrazol-5-yl)-2-[(2R)-2-methylpiperazin-1-yl]quinazolin-4-amine


Mass: 365.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N7
#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.: 58 / 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: 2.81 Å3/Da / Density % sol: 56.18 % / Description: hexagonal
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Na-acetate pH 5-6.5, 2% PEG-4000, 15% MPD / PH range: 5.5-6.5 / Temp details: 289-291

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 13136 / % possible obs: 99.9 % / Redundancy: 19.5 % / Biso Wilson estimate: 44.18 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.016 / Rrim(I) all: 0.071 / Χ2: 1.245 / Net I/av σ(I): 53.6 / Net I/σ(I): 8.1
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 4 / Num. unique obs: 666 / CC1/2: 0.947 / Rpim(I) all: 0.151 / Rrim(I) all: 0.673 / Χ2: 0.35 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B9P

3b9p


Resolution: 2.425→39.614 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.48
RfactorNum. reflection% reflection
Rfree0.2402 1290 9.86 %
Rwork0.199 --
obs0.203 13089 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.8 Å2 / Biso mean: 64.8662 Å2 / Biso min: 32.65 Å2
Refinement stepCycle: final / Resolution: 2.425→39.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 40 58 2129
Biso mean--65.68 68.81 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042101
X-RAY DIFFRACTIONf_angle_d0.8722866
X-RAY DIFFRACTIONf_chiral_restr0.28352
X-RAY DIFFRACTIONf_plane_restr0.007366
X-RAY DIFFRACTIONf_dihedral_angle_d12.7581264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4254-2.52250.37121450.27571292143799
2.5225-2.63730.31351450.256813031448100
2.6373-2.77630.31271440.247413001444100
2.7763-2.95010.25761460.230413221468100
2.9501-3.17780.27511450.241513041449100
3.1778-3.49750.28331440.205313221466100
3.4975-4.00310.21761400.187413021442100
4.0031-5.04190.20251380.168813271465100
5.0419-39.6190.21751430.18711327147099

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