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- PDB-4bzi: The structure of the COPII coat assembled on membranes -

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Basic information

Entry
Database: PDB / ID: 4bzi
TitleThe structure of the COPII coat assembled on membranes
Components
  • (SEC24P) x 2
  • SAR1P
  • SEC23P
KeywordsTRANSPORT PROTEIN / SECRETION / TRAFFICKING / SEC23 / SEC24 / SAR1
Function / homology
Function and homology information


Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / regulation of COPII vesicle coating / positive regulation of ER to Golgi vesicle-mediated transport / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-mediated vesicle transport / nuclear envelope organization / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat ...Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / regulation of COPII vesicle coating / positive regulation of ER to Golgi vesicle-mediated transport / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-mediated vesicle transport / nuclear envelope organization / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / signal sequence binding / mitochondrial fission / mitochondrial membrane organization / fungal-type vacuole membrane / reticulophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / vesicle-mediated transport / GTPase activator activity / SNARE binding / macroautophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / ER to Golgi transport vesicle membrane / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / mitochondrion / zinc ion binding
Similarity search - Function
small GTPase SAR1 family profile. / Small GTPase superfamily, SAR1-type / Protein transport protein Sec23 / Sec23, C-terminal / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily ...small GTPase SAR1 family profile. / Small GTPase superfamily, SAR1-type / Protein transport protein Sec23 / Sec23, C-terminal / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Sec23/Sec24 beta-sandwich domain / Gelsolin-like domain superfamily / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Gelsolin-like domain / Gelsolin repeat / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor A-like domain superfamily / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Sec24p / Small COPII coat GTPase SAR1 / : / Protein transport protein SEC23 / Small COPII coat GTPase SAR1 / Protein transport protein SEC24
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 23 Å
AuthorsZanetti, G. / Prinz, S. / Daum, S. / Meister, A. / Schekman, R. / Bacia, K. / Briggs, J.A.G.
CitationJournal: Elife / Year: 2013
Title: The structure of the COPII transport-vesicle coat assembled on membranes.
Authors: Giulia Zanetti / Simone Prinz / Sebastian Daum / Annette Meister / Randy Schekman / Kirsten Bacia / John A G Briggs /
Abstract: Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, ...Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, linking them to the outer COPII components that form a cage around the vesicle. Regulated flexibility in coat architecture is essential for transport of a variety of differently sized cargoes, but structural data on the assembled coat has not been available. We have used cryo-electron tomography and subtomogram averaging to determine the structure of the complete, membrane-assembled COPII coat. We describe a novel arrangement of the outer coat and find that the inner coat can assemble into regular lattices. The data reveal how coat subunits interact with one another and with the membrane, suggesting how coordinated assembly of inner and outer coats can mediate and regulate packaging of vesicles ranging from small spheres to large tubular carriers. DOI:http://dx.doi.org/10.7554/eLife.00951.001.
History
DepositionJul 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Derived calculations / Refinement description
Category: em_3d_fitting / em_software / pdbx_struct_assembly_gen
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 1.4Oct 3, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: SEC23P
B: SAR1P
D: SEC23P
E: SEC24P
F: SEC24P
G: SEC23P
J: SAR1P
K: SAR1P
L: SEC24P
M: SEC24P
N: SEC24P
O: SEC24P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)945,06524
Polymers943,03312
Non-polymers2,03212
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 12 molecules ADGBJKELMFNO

#1: Protein SEC23P


Mass: 85463.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PTKY9 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY3764 / References: UniProt: E7QAP0, UniProt: P15303*PLUS
#2: Protein SAR1P


Mass: 21472.564 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PTY40 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): KBB1012 / References: UniProt: C8ZIG2, UniProt: P20606*PLUS
#3: Protein SEC24P


Mass: 103733.250 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PTKY9 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY3764 / References: UniProt: C8ZAD6, UniProt: P40482*PLUS
#4: Protein SEC24P


Mass: 103675.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PTKY9 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY3764 / References: UniProt: C8ZAD6, UniProt: P40482*PLUS

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Non-polymers , 3 types, 12 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: SEC23-23-SAR1 / Type: COMPLEX
Buffer solutionName: MM HEPES, 50 MM KOAC, 1.2 MM MGCL2 / pH: 6.8 / Details: MM HEPES, 50 MM KOAC, 1.2 MM MGCL2
SpecimenConc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Sep 18, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 19500 X / Nominal defocus max: 3200 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm
Specimen holderTilt angle max: 60 ° / Tilt angle min: -60 °
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN MULTISCAN
Image scansNum. digital images: 26

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2AV33D reconstruction
3MATLAB3D reconstruction
4TOM Toolbox3D reconstruction
CTF correctionDetails: EACH TILTED IMAGE WITHIN TOMOGRAM
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: SUBTOMOGRAM ALIGNMENT AND AVERAGING / Resolution: 23 Å / Num. of particles: 15000 / Actual pixel size: 4.3 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2428. (DEPOSITION ID: 11856).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 1M2O
RefinementHighest resolution: 23 Å
Refinement stepCycle: LAST / Highest resolution: 23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39049 0 105 0 39154

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