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- PDB-5lg4: Crystal structure of the Sec3/Sso2 complex at 2.9 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5lg4
TitleCrystal structure of the Sec3/Sso2 complex at 2.9 angstrom resolution
Components
  • Exocyst complex component SEC3Exocyst
  • Protein SSO2
KeywordsSTRUCTURAL PROTEIN / exocyst / coiled-coil / Sec3 / Sso2
Function / homology
Function and homology information


vesicle fusion to plasma membrane / Disinhibition of SNARE formation / ascospore-type prospore assembly / exocyst assembly / exocyst localization / Insulin processing / endoplasmic reticulum inheritance / exocyst / Golgi vesicle fusion to target membrane / trans-Golgi Network Vesicle Budding ...vesicle fusion to plasma membrane / Disinhibition of SNARE formation / ascospore-type prospore assembly / exocyst assembly / exocyst localization / Insulin processing / endoplasmic reticulum inheritance / exocyst / Golgi vesicle fusion to target membrane / trans-Golgi Network Vesicle Budding / prospore membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / COPII-mediated vesicle transport / incipient cellular bud site / vesicle fusion / cellular bud tip / vesicle docking / SNARE complex / SNAP receptor activity / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck / phosphatidic acid binding / mating projection tip / 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 / 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 / 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: 2.9 Å
AuthorsZhang, Y.B. / Dong, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP24383-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
DepositionJul 5, 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 1.2Jan 10, 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: Exocyst complex component SEC3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1297
Polymers79,7443
Non-polymers3844
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-47 kcal/mol
Surface area30080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.123, 84.123, 237.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein SSO2


Mass: 22718.232 Da / Num. of mol.: 1
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: Enterobacteria phage L1 (virus) / References: UniProt: P39926
#2: Protein Exocyst complex component SEC3 / Exocyst / Protein PSL1


Mass: 28513.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: SEC3, PSL1, YER008C / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P33332
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: The small rod-like crystals were obtained in a condition containing 0.1 M Tris-HCl (pH 8.5) and 2 M (NH4)2SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 75872 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.158 / Net I/σ(I): 15.3
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.64 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.615 / % possible all: 99.4

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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.pdb, 1IFO.pdb

3a58

1ifo


Resolution: 2.9→19.828 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.83
RfactorNum. reflection% reflection
Rfree0.281 1628 8.3 %
Rwork0.2602 --
obs0.2619 19614 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4401 0 20 0 4421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024497
X-RAY DIFFRACTIONf_angle_d0.4166061
X-RAY DIFFRACTIONf_dihedral_angle_d11.1722774
X-RAY DIFFRACTIONf_chiral_restr0.038664
X-RAY DIFFRACTIONf_plane_restr0.002784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-2.98521321454X-RAY DIFFRACTION100
2.9852-3.08120.38041311454X-RAY DIFFRACTION100
3.0812-3.19090.36331331468X-RAY DIFFRACTION100
3.1909-3.31810.32671331474X-RAY DIFFRACTION100
3.3181-3.46830.321331462X-RAY DIFFRACTION100
3.4683-3.65010.35881341494X-RAY DIFFRACTION100
3.6501-3.87720.33491341471X-RAY DIFFRACTION100
3.8772-4.1740.2921351493X-RAY DIFFRACTION100
4.174-4.58930.28131371515X-RAY DIFFRACTION100
4.5893-5.24270.2851371522X-RAY DIFFRACTION100
5.2427-6.56510.29381400.27491539X-RAY DIFFRACTION100
6.5651-19.8280.20011490.20421640X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.8315 Å / Origin y: -37.4244 Å / Origin z: 32.2247 Å
111213212223313233
T0.7156 Å2-0.0743 Å20.0199 Å2-0.7647 Å2-0.1355 Å2--0.7714 Å2
L1.0409 °2-0.4564 °20.4759 °2-1.1808 °2-0.2167 °2--1.1891 °2
S-0.0505 Å °0.1706 Å °-0.1958 Å °-0.0557 Å °-0.0141 Å °0.0382 Å °0.3072 Å °-0.116 Å °0.0571 Å °
Refinement TLS groupSelection details: all

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