[English] 日本語
Yorodumi
- PDB-1gl2: Crystal structure of an endosomal SNARE core complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gl2
TitleCrystal structure of an endosomal SNARE core complex
Components
  • ENDOBREVINVesicle-associated membrane protein 8
  • SYNTAXIN 7
  • SYNTAXIN 8
  • VESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 1
KeywordsMEMBRANE PROTEIN / MEMBRANE FUSION PROTEIN COMPLEX / COILED COIL / TRANSMEMBRANE / TRANSPORT
Function / homology
Function and homology information


zymogen granule exocytosis / positive regulation of pancreatic amylase secretion / organelle localization / tertiary granule / mucin granule / negative regulation of secretion by cell / positive regulation of receptor localization to synapse / positive regulation of histamine secretion by mast cell / : / zymogen granule ...zymogen granule exocytosis / positive regulation of pancreatic amylase secretion / organelle localization / tertiary granule / mucin granule / negative regulation of secretion by cell / positive regulation of receptor localization to synapse / positive regulation of histamine secretion by mast cell / : / zymogen granule / vesicle fusion with Golgi apparatus / organelle assembly / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Golgi to vacuole transport / mucus secretion / vesicle fusion / vesicle docking / Platelet degranulation / chloride channel inhibitor activity / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome to late endosome transport / retrograde transport, endosome to Golgi / SNARE complex assembly / syntaxin binding / Neutrophil degranulation / azurophil granule / azurophil granule membrane / autophagosome membrane docking / endosome to lysosome transport / autophagosome maturation / regulation of endocytosis / endocytic vesicle / immunological synapse / endomembrane system / regulation of protein localization to plasma membrane / phagocytic vesicle / vesicle-mediated transport / SNARE binding / secretory granule membrane / secretory granule / macroautophagy / intracellular protein transport / trans-Golgi network / ER to Golgi transport vesicle membrane / recycling endosome / positive regulation of T cell mediated cytotoxicity / cellular response to type II interferon / recycling endosome membrane / synaptic vesicle / late endosome / protein transport / late endosome membrane / midbody / early endosome membrane / basolateral plasma membrane / protein-containing complex assembly / defense response to virus / vesicle / membrane fusion / lysosome / membrane => GO:0016020 / early endosome / endosome / symbiont entry into host cell / lysosomal membrane / intracellular membrane-bounded organelle / neuronal cell body / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syntaxin-8, SNARE domain / Syntaxin-like protein / Snare region anchored in the vesicle membrane C-terminus / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE, N-terminal domain superfamily / Vesicle transport v-SNARE protein N-terminus / Synaptobrevin/Vesicle-associated membrane protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin N-terminal domain ...Syntaxin-8, SNARE domain / Syntaxin-like protein / Snare region anchored in the vesicle membrane C-terminus / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE, N-terminal domain superfamily / Vesicle transport v-SNARE protein N-terminus / Synaptobrevin/Vesicle-associated membrane protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Synaptobrevin signature. / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Synaptobrevin-like / Syntaxin/epimorphin, conserved site / Synaptobrevin / Syntaxin / epimorphin family signature. / v-SNARE, coiled-coil homology domain / v-SNARE coiled-coil homology domain profile. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Syntaxin-7 / Vesicle transport through interaction with t-SNAREs homolog 1B / Vesicle-associated membrane protein 8 / Syntaxin-8
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAntonin, W. / Becker, S. / Jahn, R. / Schneider, T.R.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal Structure of the Endosomal Snare Complex Reveals Common Structural Principles of All Snares.
Authors: Antonin, W. / Fasshauer, D. / Becker, S. / Jahn, R. / Schneider, T.R.
History
DepositionAug 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0May 30, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_struct_assembly ...atom_site / pdbx_struct_assembly / pdbx_struct_assembly_prop / struct
Item: _pdbx_struct_assembly.method_details / _struct.title
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOBREVIN
B: SYNTAXIN 7
C: VESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 1
D: SYNTAXIN 8


Theoretical massNumber of molelcules
Total (without water)29,5844
Polymers29,5844
Non-polymers00
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-91 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.700, 41.100, 51.500
Angle α, β, γ (deg.)90.00, 109.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ENDOBREVIN / Vesicle-associated membrane protein 8


Mass: 7361.149 Da / Num. of mol.: 1 / Fragment: CORE FRAGMENT, RESIDUES 6-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9WUF4
#2: Protein SYNTAXIN 7 /


Mass: 7325.043 Da / Num. of mol.: 1 / Fragment: CORE FRAGMENT, RESIDUES 169-229
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O70439
#3: Protein VESICLE TRANSPORT V-SNARE PROTEIN VTI1-LIKE 1 / VTI1B


Mass: 7551.417 Da / Num. of mol.: 1 / Fragment: CORE FRAGMENT, RESIDUES 140-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O88384
#4: Protein SYNTAXIN 8 /


Mass: 7346.017 Da / Num. of mol.: 1 / Fragment: CORE FRAGMENT, RESIDUES 149-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9Z2Q7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity % sol: 30 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.2
Details: PROTEIN SOLUTION: 20 MG/ML OF QUATERNARY COMPLEX IN 20MM TRIS-HCL AT PH 7.4 WELL SOLUTION: 0.1M NA-ACETATE AT PH 5.2, 2.5 M NA-FORMIAT, 15% GLYCEROL HANGING DROPS WITH 2MUL + 2 MUL
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMTris-HCl1droppH7.4
30.1 Msodium acetate1reservoirpH5.2
42.5 Msodium formate1reservoir
515 %(v/v)glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS M18X / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2001 / Details: COSMIC MIRRORS CMF12-38CU6
RadiationMonochromator: COSMIC MIRRORS CMF12-38CU6 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 71259 / % possible obs: 93.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.0345 / Net I/σ(I): 30.57
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 11.35 / % possible all: 88.8
Reflection
*PLUS
Num. obs: 14969 / Num. measured all: 71259 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 88.8 % / Redundancy: 3.6 % / Mean I/σ(I) obs: 11.4

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SFC

1sfc


Resolution: 1.9→14.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.224 737 5 %RANDOM
Rwork0.176 ---
obs0.176 14797 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.7879 Å2 / ksol: 0.418194 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.34 Å20 Å21.15 Å2
2---2.53 Å20 Å2
3----4.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 0 234 2030
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d13.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.58
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it3.982.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.266 118 5.2 %
Rwork0.196 2143 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg13.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.58

+
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