[English] 日本語
Yorodumi
- PDB-5hjn: Crystal structure of the TBC domain of Skywalker/TBC1D24 from Dro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hjn
TitleCrystal structure of the TBC domain of Skywalker/TBC1D24 from Drosophila melanogaster
ComponentsLD10117p
KeywordsSIGNALING PROTEIN / TBC / RabGAP
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 / postsynapse / chemical synaptic transmission / response to oxidative stress / endosome membrane / lipid binding / synapse / nucleus / 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 / SAD / Resolution: 2.501 Å
AuthorsFischer, B. / Paesmans, J. / Versees, W.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Belgium
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Skywalker-TBC1D24 has a lipid-binding pocket mutated in epilepsy and required for synaptic function.
Authors: Fischer, B. / Luthy, K. / Paesmans, J. / De Koninck, C. / Maes, I. / Swerts, J. / Kuenen, S. / Uytterhoeven, V. / Verstreken, P. / Versees, W.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LD10117p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1932
Polymers43,0971
Non-polymers961
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-13 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.251, 87.251, 187.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein LD10117p / Skywalker / isoform A / isoform B / isoform H


Mass: 43096.793 Da / Num. of mol.: 1 / Fragment: TBC domain, UNP residues 1-353
Source method: isolated from a genetically manipulated source
Details: Contains a N-Terminal His-Tag / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sky, CG9339, Dmel_CG9339 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9VIH7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4.14 Å3/Da / Density % sol: 70.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 3350, ammonium citrate tribasic

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.5→43.89 Å / Num. obs: 25773 / % possible obs: 99.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 17.06

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.501→43.89 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.26
RfactorNum. reflection% reflection
Rfree0.2647 1289 5 %
Rwork0.2178 --
obs0.2201 25764 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→43.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 5 47 2554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032582
X-RAY DIFFRACTIONf_angle_d0.6993503
X-RAY DIFFRACTIONf_dihedral_angle_d14.309953
X-RAY DIFFRACTIONf_chiral_restr0.029389
X-RAY DIFFRACTIONf_plane_restr0.004435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5012-2.60130.30621380.28712623X-RAY DIFFRACTION99
2.6013-2.71970.31111410.24892674X-RAY DIFFRACTION100
2.7197-2.8630.26751400.23722660X-RAY DIFFRACTION100
2.863-3.04240.26791420.2282693X-RAY DIFFRACTION100
3.0424-3.27720.27851410.23232688X-RAY DIFFRACTION100
3.2772-3.60690.25711430.22092723X-RAY DIFFRACTION100
3.6069-4.12840.27111440.19962732X-RAY DIFFRACTION100
4.1284-5.20010.23691460.19282764X-RAY DIFFRACTION100
5.2001-43.89830.26821540.22232918X-RAY DIFFRACTION99

+
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://pdbjlvh1.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