[English] 日本語
Yorodumi
- PDB-6p11: Structure of spastin AAA domain (T692A mutant) in complex with JN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p11
TitleStructure of spastin AAA domain (T692A 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


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: 2.15 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Drosophila melanogaster Spastin AAA domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9004
Polymers34,2911
Non-polymers6093
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, differential scanning fluorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-28 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.446, 79.446, 97.171
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

-
Components

#1: Protein Drosophila melanogaster Spastin AAA domain / 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
#2: Chemical ChemComp-SO4 / SULFATE ION


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


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.: 178 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 56.99 % / Description: hexagonal
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

-
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: Oct 13, 2018
Diffraction measurementDetails: 0.20 degrees, 0.01 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: 0.035 / Number: 103752
ReflectionResolution: 2.15→50 Å / Num. obs: 18983 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 46.9707656484 Å2 / Rmerge(I) obs: 0.035 / Net I/av σ(I): 37.375 / Net I/σ(I): 10.6
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.667 / Num. unique obs: 940 / % possible all: 99.9
Cell measurementReflection used: 103752

-
Processing

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

3b9p


Resolution: 2.15→39.6875727494 Å / SU ML: 0.284715253732 / Cross valid method: FREE R-VALUE / σ(F): 1.38897488545 / Phase error: 26.7572588333
RfactorNum. reflection% reflection
Rfree0.240981213524 1889 9.97149493243 %
Rwork0.212595700008 --
obs0.215347370249 18944 99.8103266596 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.8610370905 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.6875727494 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 40 178 2245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001664674850522144
X-RAY DIFFRACTIONf_angle_d0.4132080231942929
X-RAY DIFFRACTIONf_chiral_restr0.0372083766985350
X-RAY DIFFRACTIONf_plane_restr0.00231430244276373
X-RAY DIFFRACTIONf_dihedral_angle_d11.71483246841703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1492-2.20730.3380152261331470.2994303851491326X-RAY DIFFRACTION99.8644067797
2.2073-2.27230.3369592502651440.2796906296011289X-RAY DIFFRACTION100
2.2723-2.34560.331425336011480.2634769875721302X-RAY DIFFRACTION99.9310820124
2.3456-2.42940.3123276752481400.2739664760221297X-RAY DIFFRACTION100
2.4294-2.52670.2943014565311450.2666320120311309X-RAY DIFFRACTION99.9312714777
2.5267-2.64170.3119250681381430.2690441686891315X-RAY DIFFRACTION99.8630136986
2.6417-2.78090.265339934111490.2629421724771315X-RAY DIFFRACTION100
2.7809-2.95510.2500054552571490.2422658828341315X-RAY DIFFRACTION100
2.9551-3.18320.2936954688251470.2298036115521317X-RAY DIFFRACTION99.9317406143
3.1832-3.50330.2244529666651520.2187862749321302X-RAY DIFFRACTION99.7940974605
3.5033-4.00980.2276044057151410.1879817422751311X-RAY DIFFRACTION100
4.0098-5.05040.1948653452611430.1784053729681325X-RAY DIFFRACTION99.796057104
5.0504-39.69430.2116701511351410.1844778189391332X-RAY DIFFRACTION98.5284280936

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more