[English] 日本語
Yorodumi
- PDB-6r82: Crystal structure of the TLDc domain of Skywalker/TBC1D24 from Dr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6r82
TitleCrystal structure of the TLDc domain of Skywalker/TBC1D24 from Drosophila melanogaster
ComponentsGTPase-activating protein skywalker
KeywordsUNKNOWN FUNCTION / tldc domain
Function / homology
Function and homology information


synaptic vesicle endosomal processing / negative regulation of synaptic vesicle recycling / synaptic vesicle recycling via endosome / vesicle-mediated transport in synapse / neuromuscular synaptic transmission / negative regulation of neurotransmitter secretion / regulation of GTPase activity / GTPase activator activity / neuromuscular junction / terminal bouton ...synaptic vesicle endosomal processing / negative regulation of synaptic vesicle recycling / synaptic vesicle recycling via endosome / vesicle-mediated transport in synapse / neuromuscular synaptic transmission / negative regulation of neurotransmitter secretion / regulation of GTPase activity / GTPase activator activity / neuromuscular junction / terminal bouton / synaptic vesicle membrane / neuron projection development / chemical synaptic transmission / postsynapse / endosome membrane / lipid binding / synapse / cytoplasm
Similarity search - Function
TLDc domain profile. / TLDc domain / TLD / domain in TBC and LysM domain containing proteins / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile.
Similarity search - Domain/homology
GTPase-activating protein skywalker
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.046 Å
AuthorsFischer, B. / Paesmans, J. / Versees, W.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders Belgium
CitationJournal: Brain / Year: 2019
Title: TBC1D24-TLDc-related epilepsy exercise-induced dystonia: rescue by antioxidants in a disease model.
Authors: Luthy, K. / Mei, D. / Fischer, B. / De Fusco, M. / Swerts, J. / Paesmans, J. / Parrini, E. / Lubarr, N. / Meijer, I.A. / Mackenzie, K.M. / Lee, W.T. / Cittaro, D. / Aridon, P. / Schoovaerts, ...Authors: Luthy, K. / Mei, D. / Fischer, B. / De Fusco, M. / Swerts, J. / Paesmans, J. / Parrini, E. / Lubarr, N. / Meijer, I.A. / Mackenzie, K.M. / Lee, W.T. / Cittaro, D. / Aridon, P. / Schoovaerts, N. / Versees, W. / Verstreken, P. / Casari, G. / Guerrini, R.
History
DepositionMar 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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
A: GTPase-activating protein skywalker
B: GTPase-activating protein skywalker


Theoretical massNumber of molelcules
Total (without water)43,1472
Polymers43,1472
Non-polymers00
Water2,144119
1
A: GTPase-activating protein skywalker


Theoretical massNumber of molelcules
Total (without water)21,5731
Polymers21,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase-activating protein skywalker


Theoretical massNumber of molelcules
Total (without water)21,5731
Polymers21,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.483, 89.483, 135.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein GTPase-activating protein skywalker


Mass: 21573.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sky, CG9339 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VIH7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 28% PEG 3350, 0.1 M Hepes pH 7.5 and 0.6M ammonium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.046→42.38 Å / Num. obs: 35238 / % possible obs: 99.8 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 19.2
Reflection shellResolution: 2.046→2.17 Å / Rmerge(I) obs: 0.972 / Num. unique obs: 5519 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ACJ

4acj


Resolution: 2.046→38.369 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.57
RfactorNum. reflection% reflection
Rfree0.225 1762 5 %
Rwork0.1948 --
obs0.1963 35235 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.046→38.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 0 119 2952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082915
X-RAY DIFFRACTIONf_angle_d0.8673949
X-RAY DIFFRACTIONf_dihedral_angle_d8.3021676
X-RAY DIFFRACTIONf_chiral_restr0.054414
X-RAY DIFFRACTIONf_plane_restr0.005500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0465-2.10180.37451300.3142467X-RAY DIFFRACTION98
2.1018-2.16360.33121330.26592524X-RAY DIFFRACTION100
2.1636-2.23350.26561330.24782533X-RAY DIFFRACTION100
2.2335-2.31330.24351350.22812551X-RAY DIFFRACTION100
2.3133-2.40590.25891330.21882536X-RAY DIFFRACTION100
2.4059-2.51530.26731350.20662551X-RAY DIFFRACTION100
2.5153-2.64790.3171340.22742554X-RAY DIFFRACTION100
2.6479-2.81380.27651350.22312565X-RAY DIFFRACTION100
2.8138-3.0310.26521360.23422576X-RAY DIFFRACTION100
3.031-3.33580.26831360.22322586X-RAY DIFFRACTION100
3.3358-3.81810.23011360.1862593X-RAY DIFFRACTION100
3.8181-4.8090.15191400.15432649X-RAY DIFFRACTION100
4.809-38.37610.18611460.16522788X-RAY DIFFRACTION100

+
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