[English] 日本語
Yorodumi
- PDB-5m4y: Crystal structure of the Sec3/Sso2 complex at 2.20 angstrom resolution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m4y
TitleCrystal structure of the Sec3/Sso2 complex at 2.20 angstrom resolution
Components
  • Exocyst complex component SEC3
  • Protein SSO2
KeywordsSTRUCTURAL PROTEIN / exocyst / Sec3 / Sso2
Function / homology
Function and homology information


exocyst assembly / exocyst localization / endoplasmic reticulum inheritance / Disinhibition of SNARE formation / vesicle fusion to plasma membrane / ascospore-type prospore assembly / exocyst / Golgi vesicle fusion to target membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / trans-Golgi Network Vesicle Budding ...exocyst assembly / exocyst localization / endoplasmic reticulum inheritance / Disinhibition of SNARE formation / vesicle fusion to plasma membrane / ascospore-type prospore assembly / exocyst / Golgi vesicle fusion to target membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / trans-Golgi Network Vesicle Budding / prospore membrane / incipient cellular bud site / cellular bud tip / vesicle docking / SNARE complex / SNAP receptor activity / vesicle fusion / cellular bud neck / Golgi to plasma membrane transport / phosphatidic acid binding / mating projection tip / vesicle docking involved in exocytosis / exocytosis / phosphatidylinositol-4,5-bisphosphate binding / endomembrane system / SNARE binding / cell periphery / intracellular protein transport / small GTPase binding / protein transport / Golgi membrane / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
PH-domain like - #90 / Exocyst complex component Sec3, C-terminal / Exocyst complex component Sec3, PIP2-binding N-terminal domain / : / Exocyst complex component Sec3, coiled-coil / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Sec3, C-terminal / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Syntaxin ...PH-domain like - #90 / Exocyst complex component Sec3, C-terminal / Exocyst complex component Sec3, PIP2-binding N-terminal domain / : / Exocyst complex component Sec3, coiled-coil / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Exocyst complex component Sec3, C-terminal / Exocyst complex component SEC3 N-terminal PIP2 binding PH / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / 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 / PH-domain like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Exocyst complex component SEC3 / Protein SSO2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhang, Y.B. / Dong, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP24929-B21 Austria
CitationJournal: Nat Commun / Year: 2017
Title: Sec3 promotes the initial binary t-SNARE complex assembly and membrane fusion.
Authors: Yue, P. / Zhang, Y. / Mei, K. / Wang, S. / Lesigang, J. / Zhu, Y. / Dong, G. / Guo, W.
History
DepositionOct 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Oct 16, 2019Group: Atomic model / Data collection / Category: atom_site / reflns_shell / Item: _atom_site.occupancy
Revision 2.1Jan 17, 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: Protein SSO2
B: Exocyst complex component SEC3
C: Protein SSO2
D: Exocyst complex component SEC3
E: Protein SSO2
F: Exocyst complex component SEC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,8147
Polymers158,7226
Non-polymers921
Water5,855325
1
A: Protein SSO2
B: Exocyst complex component SEC3


Theoretical massNumber of molelcules
Total (without water)52,9072
Polymers52,9072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein SSO2
D: Exocyst complex component SEC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9993
Polymers52,9072
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Protein SSO2
F: Exocyst complex component SEC3


Theoretical massNumber of molelcules
Total (without water)52,9072
Polymers52,9072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.145, 135.803, 185.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-476-

HOH

-
Components

#1: Protein Protein SSO2


Mass: 24394.135 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SSO2, YMR183C, YM8010.13C / Production host: Escherichia coli BL21(DE3) / References: UniProt: P39926
#2: Protein Exocyst complex component SEC3 / Protein PSL1


Mass: 28513.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SEC3, PSL1, YER008C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33332
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.01 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES (pH 7.0), 0.2 M NaCl, and 25% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 62754 / % possible obs: 99.4 % / Redundancy: 6.5 % / Net I/σ(I): 13.2

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A58, 1IFO

3a58

1ifo


Resolution: 2.2→19.978 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.83
RfactorNum. reflection% reflection
Rfree0.264 1735 2.67 %
Rwork0.2286 --
obs0.2295 64891 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8680 0 6 325 9011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028819
X-RAY DIFFRACTIONf_angle_d0.42211872
X-RAY DIFFRACTIONf_dihedral_angle_d14.2875488
X-RAY DIFFRACTIONf_chiral_restr0.0361303
X-RAY DIFFRACTIONf_plane_restr0.0021559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.26470.36421420.34755193X-RAY DIFFRACTION100
2.2647-2.33770.29831440.31975203X-RAY DIFFRACTION100
2.3377-2.42110.32151440.30245241X-RAY DIFFRACTION100
2.4211-2.51780.31481430.2955214X-RAY DIFFRACTION100
2.5178-2.63220.34181430.28855204X-RAY DIFFRACTION100
2.6322-2.77060.31091450.295243X-RAY DIFFRACTION100
2.7706-2.94370.32781430.26645227X-RAY DIFFRACTION100
2.9437-3.17020.31391450.26165246X-RAY DIFFRACTION100
3.1702-3.48770.27561460.23085295X-RAY DIFFRACTION100
3.4877-3.98880.24941450.20345281X-RAY DIFFRACTION100
3.9888-5.01240.21111470.17745348X-RAY DIFFRACTION100
5.0124-19.97870.21451480.19495461X-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