[English] 日本語
Yorodumi
- PDB-8qqf: TBC1D23 PH domain complexed with STX16 TLY motif -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qqf
TitleTBC1D23 PH domain complexed with STX16 TLY motif
Components
  • Syntaxin-16
  • TBC1 domain family member 23
KeywordsENDOCYTOSIS / Tether / vesicle-coat / endosome to golgi transport / snare
Function / homology
Function and homology information


vesicle tethering to Golgi / Golgi cisterna / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / embryonic brain development / endocytic recycling ...vesicle tethering to Golgi / Golgi cisterna / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / embryonic brain development / endocytic recycling / retrograde transport, endosome to Golgi / syntaxin binding / endomembrane system / vesicle-mediated transport / SNARE binding / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / brain development / synaptic vesicle membrane / neuron projection development / cytoplasmic vesicle / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / perinuclear region of cytoplasm / Golgi apparatus / membrane / cytoplasm / cytosol
Similarity search - Function
TBC1 domain family member 23 / TBC1 domain family member 23, C-terminal domain / TBC1 domain family member 23 C-terminal / 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. / Syntaxin / Syntaxin, N-terminal domain ...TBC1 domain family member 23 / TBC1 domain family member 23, C-terminal domain / TBC1 domain family member 23 C-terminal / 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. / Syntaxin / Syntaxin, N-terminal domain / Syntaxin / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain
Similarity search - Domain/homology
PHOSPHATE ION / Syntaxin-16 / TBC1 domain family member 23
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKaufman, J.G. / Owen, D.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N013433/1 United Kingdom
Wellcome Trust207455/Z/17/Z United Kingdom
CitationJournal: Sci Adv / Year: 2024
Title: Cargo selective vesicle tethering: The structural basis for binding of specific cargo proteins by the Golgi tether component TBC1D23.
Authors: Cattin-Ortola, J. / Kaufman, J.G.G. / Gillingham, A.K. / Wagstaff, J.L. / Peak-Chew, S.Y. / Stevens, T.J. / Boulanger, J. / Owen, D.J. / Munro, S.
History
DepositionOct 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TBC1 domain family member 23
C: TBC1 domain family member 23
B: Syntaxin-16
D: Syntaxin-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,89912
Polymers31,1484
Non-polymers7518
Water2,414134
1
A: TBC1 domain family member 23
B: Syntaxin-16
hetero molecules


  • defined by author&software
  • Evidence: isothermal titration calorimetry, demonstrated direct binding in a 1:1 stoichiometry, mass spectrometry, experiements discovered an interaction between these proteins, microscopy, live cell ...Evidence: isothermal titration calorimetry, demonstrated direct binding in a 1:1 stoichiometry, mass spectrometry, experiements discovered an interaction between these proteins, microscopy, live cell imaging reveiled structurally designed point mutations that ablate interaction in ITC affect the localisation of cargos such as STX16 and CPD in vivo
  • 15.8 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)15,7644
Polymers15,5742
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-10 kcal/mol
Surface area7570 Å2
MethodPISA
2
C: TBC1 domain family member 23
D: Syntaxin-16
hetero molecules


  • defined by author&software
  • Evidence: isothermal titration calorimetry, demonstrated direct binding in a 1:1 stoichiometry, mass spectrometry, experiements discovered an interaction between these proteins, microscopy, live cell ...Evidence: isothermal titration calorimetry, demonstrated direct binding in a 1:1 stoichiometry, mass spectrometry, experiements discovered an interaction between these proteins, microscopy, live cell imaging reveiled structurally designed point mutations that ablate interaction in ITC affect the localisation of cargos such as STX16 and CPD in vivo
  • 16.1 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)16,1358
Polymers15,5742
Non-polymers5616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-20 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.159, 134.159, 123.542
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

-
Components

#1: Protein TBC1 domain family member 23 / HCV non-structural protein 4A-transactivated protein 1


Mass: 13989.394 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D23, NS4ATP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NUY8
#2: Protein/peptide Syntaxin-16 / Syn16


Mass: 1584.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14662
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.19 Å3/Da / Density % sol: 76.3 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8M Potassium phosphate dibasic, 0.1M HEPES/NaOH pH 7.5, 0.8M Sodium phosphate monobasic and 1% 1,2-Butandiol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.997 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.19→200 Å / Num. obs: 14895 / % possible obs: 94.8 % / Redundancy: 32.7 % / Biso Wilson estimate: 47.41 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 23
Reflection shellResolution: 2.19→2.48 Å / Redundancy: 82.9 % / Num. unique obs: 745 / CC1/2: 0.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXdev_svn+SVNrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→67.08 Å / SU ML: 0.2828 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1825
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 751 5.04 %RANDOM
Rwork0.2142 14136 --
obs0.2163 14887 43.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.69 Å2
Refinement stepCycle: LAST / Resolution: 2.19→67.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 43 134 2293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882203
X-RAY DIFFRACTIONf_angle_d0.9712963
X-RAY DIFFRACTIONf_chiral_restr0.0545327
X-RAY DIFFRACTIONf_plane_restr0.0074365
X-RAY DIFFRACTIONf_dihedral_angle_d19.6779820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.360.5379170.3877357X-RAY DIFFRACTION5.54
2.36-2.590.2959290.3396711X-RAY DIFFRACTION10.96
2.59-2.970.34621080.33081588X-RAY DIFFRACTION24.9
2.97-3.740.31022480.2454638X-RAY DIFFRACTION70.96
3.74-67.080.22293490.19026842X-RAY DIFFRACTION99.82

+
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