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- PDB-6p12: Structure of spastin AAA domain (wild-type) in complex with diami... -

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Basic information

Entry
Database: PDB / ID: 6p12
TitleStructure of spastin AAA domain (wild-type) in complex with diaminotriazole-based inhibitor
ComponentsDrosophila melanogaster Spastin AAA domain
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 / locomotory behavior / neuromuscular junction / 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 / 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: 1.9413185678 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

Downloads & links

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Assembly

Deposited unit
B: Drosophila melanogaster Spastin AAA domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7904
Polymers34,1921
Non-polymers5993
Water3,927218
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-27 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.672, 80.672, 96.529
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Drosophila melanogaster Spastin AAA domain / D-Spastin / Dm-Spastin / Dspastin


Mass: 34191.848 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-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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 218 / 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: 2.65 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, pH 5.0-7.0, 2% PEG4000, 15% MPD
PH range: 5.0-7.0

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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: 0.9197 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 26363 / % possible obs: 99 % / Redundancy: 6.5 % / Biso Wilson estimate: 43.2284817795 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.031 / Net I/σ(I): 16.6
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1323 / CC1/2: 0.932 / % possible all: 99.2

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Processing

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

3b9p


Resolution: 1.9413185678→40.336 Å / SU ML: 0.256993797688 / Cross valid method: FREE R-VALUE / σ(F): 1.38937703476 / Phase error: 25.154924059
RfactorNum. reflection% reflection
Rfree0.230071724697 2615 10.0103357195 %
Rwork0.19342462719 --
obs0.197067217005 26123 99.0971510944 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.7947301096 Å2
Refinement stepCycle: LAST / Resolution: 1.9413185678→40.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 41 218 2313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003812544853552169
X-RAY DIFFRACTIONf_angle_d0.5942385075042963
X-RAY DIFFRACTIONf_chiral_restr0.0377483252961356
X-RAY DIFFRACTIONf_plane_restr0.00338951409218384
X-RAY DIFFRACTIONf_dihedral_angle_d11.15796253371729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9413-1.97660.3289489009261420.3300291294921254X-RAY DIFFRACTION99.2181947406
1.9766-2.01460.3517495011441360.283252030911227X-RAY DIFFRACTION99.3440233236
2.0146-2.05580.3045641194971410.2601651340641238X-RAY DIFFRACTION99.4949494949
2.0558-2.10050.2736784850281320.2461313125051222X-RAY DIFFRACTION99.5588235294
2.1005-2.14930.2928531195311420.2404029424841246X-RAY DIFFRACTION99.6410624551
2.1493-2.20310.2874838580671370.2597698287221246X-RAY DIFFRACTION99.6397694524
2.2031-2.26260.290319224921350.2519418867071214X-RAY DIFFRACTION99.2641648271
2.2626-2.32920.3006643720291430.2459404092581237X-RAY DIFFRACTION98.3606557377
2.3292-2.40440.2882651826541300.2456564257711239X-RAY DIFFRACTION99.7813411079
2.4044-2.49030.2748356119161390.2330132984621237X-RAY DIFFRACTION99.7824510515
2.4903-2.590.2503215481481390.2268532597241244X-RAY DIFFRACTION99.8555956679
2.59-2.70780.2499154105231420.2223974422141237X-RAY DIFFRACTION99.7829232996
2.7078-2.85060.2387196976961410.2266871608761258X-RAY DIFFRACTION99.9285714286
2.8506-3.02910.3001611145871400.2182577670521249X-RAY DIFFRACTION100
3.0291-3.26290.2322644535441360.2027367464441246X-RAY DIFFRACTION99.9276934201
3.2629-3.5910.205751336781400.1827084741791247X-RAY DIFFRACTION100
3.591-4.11020.188807646721310.1624004680591219X-RAY DIFFRACTION96.5665236052
4.1102-5.17680.1817728079371350.1434488882871244X-RAY DIFFRACTION99.6387283237
5.1768-40.34470.2178368734231340.1715618552111204X-RAY DIFFRACTION93.6319104269

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