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Yorodumi- PDB-5lg4: Crystal structure of the Sec3/Sso2 complex at 2.9 angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lg4 | ||||||
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Title | Crystal structure of the Sec3/Sso2 complex at 2.9 angstrom resolution | ||||||
Components |
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Keywords | STRUCTURAL 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 / endoplasmic reticulum inheritance / exocyst / Golgi vesicle fusion to target membrane / trans-Golgi Network Vesicle Budding / prospore membrane ...vesicle fusion to plasma membrane / Disinhibition of SNARE formation / ascospore-type prospore assembly / exocyst assembly / exocyst localization / 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 / incipient cellular bud site / cellular bud tip / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / cellular bud neck / Golgi to plasma membrane transport / phosphatidic acid binding / 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 | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Zhang, Y.B. / Dong, G. | ||||||
Funding support | Austria, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lg4.cif.gz | 233.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lg4.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 5lg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lg4_validation.pdf.gz | 460 KB | Display | wwPDB validaton report |
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Full document | 5lg4_full_validation.pdf.gz | 465.9 KB | Display | |
Data in XML | 5lg4_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 5lg4_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/5lg4 ftp://data.pdbj.org/pub/pdb/validation_reports/lg/5lg4 | HTTPS FTP |
-Related structure data
Related structure data | 5m4yC 1ifoS 3a58S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | ||
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#2: Protein | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % |
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Crystal grow | Temperature: 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. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A58.pdb, 1IFO.pdb Resolution: 2.9→19.828 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.828 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -0.8315 Å / Origin y: -37.4244 Å / Origin z: 32.2247 Å
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Refinement TLS group | Selection details: all |