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- PDB-5m4y: Crystal structure of the Sec3/Sso2 complex at 2.20 angstrom resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m4y | |||||||||
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Title | Crystal structure of the Sec3/Sso2 complex at 2.20 angstrom resolution | |||||||||
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![]() | STRUCTURAL PROTEIN / exocyst / Sec3 / Sso2 | |||||||||
Function / homology | ![]() vesicle fusion to plasma membrane / Disinhibition of SNARE formation / ascospore-type prospore assembly / exocyst assembly / exocyst localization / endoplasmic reticulum inheritance / exocyst / trans-Golgi Network Vesicle Budding / Golgi vesicle fusion to target membrane / prospore membrane ...vesicle fusion to plasma membrane / Disinhibition of SNARE formation / ascospore-type prospore assembly / exocyst assembly / exocyst localization / endoplasmic reticulum inheritance / exocyst / trans-Golgi Network Vesicle Budding / Golgi vesicle fusion to target membrane / 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 / Golgi to plasma membrane transport / cellular bud neck / 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Zhang, Y.B. / Dong, G. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233 KB | Display | ![]() |
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PDB format | ![]() | 185.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.7 KB | Display | ![]() |
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Full document | ![]() | 501.3 KB | Display | |
Data in XML | ![]() | 39.3 KB | Display | |
Data in CIF | ![]() | 55.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lg4C ![]() 1ifoS ![]() 3a58S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 24394.135 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SSO2, YMR183C, YM8010.13C / Production host: Escherichia coli BL21(DE3) / References: UniProt: P39926 #2: Protein | Mass: 28513.105 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SEC3, PSL1, YER008C / Production host: ![]() ![]() #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.78 % |
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Crystal grow | Temperature: 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
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.978 Å
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Refine LS restraints |
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LS refinement shell |
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