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- PDB-6p14: Structure of spastin AAA domain (T692A mutant) in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 6p14
TitleStructure of spastin AAA domain (T692A mutant) in complex with a diaminotriazole-based inhibitor (crystal form B)
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
ACETATE ION / Chem-NKY / Spastin
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93001125684 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
A: Spastin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0676
Polymers34,2911
Non-polymers7765
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, differential scanning fluorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-29 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.294, 105.294, 65.391
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

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Protein , 1 types, 1 molecules A

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


Mass: 34291.004 Da / Num. of mol.: 1 / Fragment: 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

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Non-polymers , 5 types, 198 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.55 %
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: 0.50 degrees, 0.10 sec, detector distance 220.262 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: 0.048 / Number: 613985
ReflectionResolution: 1.93→50 Å / Num. obs: 31162 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 35.7320064918 Å2 / Rmerge(I) obs: 0.039 / Net I/av σ(I): 40.688 / Net I/σ(I): 12.4
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 6 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.957 / Num. unique obs: 1549 / % possible all: 100
Cell measurementReflection used: 613985

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Processing

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

3b9p


Resolution: 1.93001125684→34.4655518018 Å / SU ML: 0.197230604739 / Cross valid method: THROUGHOUT / σ(F): 1.37542270819 / Phase error: 19.8281104664
RfactorNum. reflection% reflection
Rfree0.199323333826 3091 9.93635077793 %
Rwork0.175237746056 --
obs0.177671751698 31108 99.8459365772 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.5359641064 Å2
Refinement stepCycle: LAST / Resolution: 1.93001125684→34.4655518018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 53 193 2199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181887843892059
X-RAY DIFFRACTIONf_angle_d1.393055623672801
X-RAY DIFFRACTIONf_chiral_restr0.104926558574330
X-RAY DIFFRACTIONf_plane_restr0.00902821481775362
X-RAY DIFFRACTIONf_dihedral_angle_d8.66531213511665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.96020.2769348888821350.2212147251811259X-RAY DIFFRACTION98.7252124646
1.9602-1.99230.2324971175711410.2013271851791246X-RAY DIFFRACTION100
1.9923-2.02660.2649040436761460.1975205250661287X-RAY DIFFRACTION100
2.0266-2.06350.2189378535321340.2096000303521273X-RAY DIFFRACTION100
2.0635-2.10320.2528636312861410.1813027986031277X-RAY DIFFRACTION100
2.1032-2.14610.2593044732161400.1793177000041253X-RAY DIFFRACTION100
2.1461-2.19280.2096151303051300.171894431041256X-RAY DIFFRACTION100
2.1928-2.24380.2156133307221420.1815015914631279X-RAY DIFFRACTION100
2.2438-2.29990.2123230356441430.1752901531931276X-RAY DIFFRACTION100
2.2999-2.3620.2161475463341380.1804231769091265X-RAY DIFFRACTION100
2.362-2.43150.2090500743921400.177224866531280X-RAY DIFFRACTION100
2.4315-2.510.2117930633861410.1698953578591273X-RAY DIFFRACTION100
2.51-2.59970.2149626767581360.168553762981267X-RAY DIFFRACTION100
2.5997-2.70370.1926411509571460.1652404482151281X-RAY DIFFRACTION100
2.7037-2.82670.1920420048151380.1706164039181262X-RAY DIFFRACTION100
2.8267-2.97570.2327331376091380.1872729173241264X-RAY DIFFRACTION100
2.9757-3.1620.200874960831450.1724140990911288X-RAY DIFFRACTION100
3.162-3.40590.1859191905741390.1705628173011279X-RAY DIFFRACTION100
3.4059-3.74830.1626676028071440.1619786186761285X-RAY DIFFRACTION100
3.7483-4.28980.1682493840231450.1605622311151277X-RAY DIFFRACTION100
4.2898-5.40130.1907345459891460.1608053064261294X-RAY DIFFRACTION99.9306037474
5.4013-34.4710.212706349541430.2031510131661296X-RAY DIFFRACTION98.0913428766

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