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- PDB-5m4y: Crystal structure of the Sec3/Sso2 complex at 2.20 angstrom resolution -

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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


Disinhibition of SNARE formation / vesicle fusion to plasma membrane / exocyst assembly / ascospore-type prospore assembly / exocyst localization / endoplasmic reticulum inheritance / Golgi vesicle fusion to target membrane / exocyst / trans-Golgi Network Vesicle Budding / prospore membrane ...Disinhibition of SNARE formation / vesicle fusion to plasma membrane / exocyst assembly / ascospore-type prospore assembly / exocyst localization / endoplasmic reticulum inheritance / Golgi vesicle fusion to target membrane / exocyst / trans-Golgi Network Vesicle Budding / prospore membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / incipient cellular bud site / vesicle fusion / cellular bud tip / vesicle docking / SNARE complex / SNAP receptor activity / Golgi to plasma membrane transport / phosphatidic acid binding / cellular bud neck / mating projection tip / vesicle docking involved in exocytosis / exocytosis / endomembrane system / phosphatidylinositol-4,5-bisphosphate binding / 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/epimorphin, conserved site / Syntaxin / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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