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- PDB-6p10: Structure of spastin AAA domain (N527C mutant) in complex with JN... -

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Basic information

Entry
Database: PDB / ID: 6p10
TitleStructure of spastin AAA domain (N527C mutant) in complex with JNJ-7706621 inhibitor
ComponentsDrosophila melanogaster Spastin AAA domain
KeywordsISOMERASE/ISOMERASE INHIBITOR / inhibitor / complex / AAA protein / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of axon extension involved in regeneration / hemocyte migration / negative regulation of synaptic assembly at neuromuscular junction / Sealing of the nuclear envelope (NE) by ESCRT-III / 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 / negative regulation of synaptic assembly at neuromuscular junction / Sealing of the nuclear envelope (NE) by ESCRT-III / 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 / positive regulation of microtubule depolymerization / mitotic spindle elongation / negative regulation of microtubule depolymerization / protein hexamerization / positive regulation of dendrite morphogenesis / mitotic sister chromatid segregation / alpha-tubulin binding / isomerase activity / lipid droplet / adult locomotory behavior / 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. / ATPase family associated with various cellular activities (AAA) ...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: 2.301 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 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation_author.identifier_ORCID
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

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Assembly

Deposited unit
B: Drosophila melanogaster Spastin AAA domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9194
Polymers34,3101
Non-polymers6093
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, differential scanning fluorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-27 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.393, 79.393, 97.261
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 Drosophila melanogaster Spastin AAA domain / D-Spastin / Dm-Spastin / Dspastin


Mass: 34310.070 Da / Num. of mol.: 1 / Fragment: UNP residues 445-758 / Mutation: N527C
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 / Sulfate


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


Mass: 394.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12F2N6O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 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 / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate, pH 5-7, 2% PEG4000, 15% MPD / PH range: 5-7

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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: 0.9181 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2017
Diffraction measurementDetails: 0.20 degrees, 0.02 sec, detector distance 200.00 mm
Method: \w scans
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9181 Å / Relative weight: 1
ReflectionAv R equivalents: 0.044 / Number: 71736
ReflectionResolution: 2.3→50 Å / Num. obs: 15364 / % possible obs: 99 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.044 / Net I/av σ(I): 32.161 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.833 / Num. unique obs: 783 / % possible all: 99.5
Cell measurementReflection used: 71736

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Processing

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

3b9p


Resolution: 2.301→39.703 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 28.2
RfactorNum. reflection% reflection
Rfree0.2518 1548 10.08 %
Rwork0.2055 --
obs0.2103 15361 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.79 Å2 / Biso mean: 61.5807 Å2 / Biso min: 31.07 Å2
Refinement stepCycle: final / Resolution: 2.301→39.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 0 40 36 2109
Biso mean--64.98 62.46 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032113
X-RAY DIFFRACTIONf_angle_d0.6322883
X-RAY DIFFRACTIONf_chiral_restr0.039351
X-RAY DIFFRACTIONf_plane_restr0.003368
X-RAY DIFFRACTIONf_dihedral_angle_d9.8341702
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3013-2.37560.31921330.24891252138599
2.3756-2.46050.34071430.259712931436100
2.4605-2.5590.30021380.244812511389100
2.559-2.67540.32831400.241112531393100
2.6754-2.81640.34831440.25311244138899
2.8164-2.99280.29521430.247412551398100
2.9928-3.22380.29551390.23281256139599
3.2238-3.54810.2641410.21611235137699
3.5481-4.0610.23241390.19611270140999
4.061-5.11480.19931430.17441251139499
5.1148-39.70910.23341450.18561253139897

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