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Yorodumi- PDB-3eg9: Crystal structure of the mammalian COPII-coat protein Sec23/24 bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eg9 | ||||||
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Title | Crystal structure of the mammalian COPII-coat protein Sec23/24 bound to the transport signal sequence of membrin | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / COPII coat / vesicle transport / transport signal sequence / Disease mutation / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transport | ||||||
Function / homology | Function and homology information vesicle fusion with Golgi apparatus / Intra-Golgi traffic / Golgi to vacuole transport / COPII-coated vesicle cargo loading / SNARE complex / SNAP receptor activity / COPII vesicle coat / COPII vesicle coating / protein targeting to vacuole / XBP1(S) activates chaperone genes ...vesicle fusion with Golgi apparatus / Intra-Golgi traffic / Golgi to vacuole transport / COPII-coated vesicle cargo loading / SNARE complex / SNAP receptor activity / COPII vesicle coat / COPII vesicle coating / protein targeting to vacuole / XBP1(S) activates chaperone genes / intra-Golgi vesicle-mediated transport / Regulation of cholesterol biosynthesis by SREBP (SREBF) / Cargo concentration in the ER / retrograde transport, endosome to Golgi / COPII-mediated vesicle transport / IRE1-mediated unfolded protein response / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / GTPase activator activity / SNARE binding / protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / ER to Golgi transport vesicle membrane / late endosome membrane / in utero embryonic development / membrane => GO:0016020 / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / Golgi apparatus / zinc ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å | ||||||
Authors | Goldberg, J. / Mancias, J.D. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Structural basis of cargo membrane protein discrimination by the human COPII coat machinery. Authors: Mancias, J.D. / Goldberg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eg9.cif.gz | 311.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eg9.ent.gz | 245.6 KB | Display | PDB format |
PDBx/mmJSON format | 3eg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eg9_validation.pdf.gz | 459.3 KB | Display | wwPDB validaton report |
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Full document | 3eg9_full_validation.pdf.gz | 522.2 KB | Display | |
Data in XML | 3eg9_validation.xml.gz | 59.6 KB | Display | |
Data in CIF | 3eg9_validation.cif.gz | 81.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/3eg9 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/3eg9 | HTTPS FTP |
-Related structure data
Related structure data | 3efoSC 3egdC 3egxC 3eh1C 3eh2C 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: 86178.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEC23A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15436 | ||
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#2: Protein | Mass: 86647.852 Da / Num. of mol.: 1 / Fragment: conserved core, UNP residues 267-1033 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SEC24D / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IYI7, UniProt: O94855*PLUS | ||
#3: Protein/peptide | Mass: 763.857 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The sequence of this 7-residue synthetic peptide occurs naturally in humans References: UniProt: O14653*PLUS | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 43252 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3EFO Resolution: 3→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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