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

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Basic information

Entry
Database: PDB / ID: 4bzk
TitleThe structure of the COPII coat assembled on membranes
Components
  • (Protein transport protein SEC13) x 2
  • Protein transport protein SEC31
KeywordsPROTEIN TRANSPORT / SECRETION / TRAFFICKING
Function / homology
Function and homology information


positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / COPII-mediated vesicle transport / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum ...positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / COPII-mediated vesicle transport / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / COPII vesicle coat / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / mating projection tip / endoplasmic reticulum organization / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / vacuolar membrane / nucleocytoplasmic transport / endoplasmic reticulum exit site / positive regulation of TOR signaling / mRNA transport / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / cell periphery / protein import into nucleus / nuclear envelope / protein transport / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum
Similarity search - Function
Protein transport protein SEC31 / Protein transport protein SEC31 / Protein transport protein SEC31-like / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Ancestral coatomer element 1, Sec16/Sec31 / Sec16 Sec23-binding domain / Sec13/Seh1 family / WD domain, G-beta repeat / WD40 repeat, conserved site ...Protein transport protein SEC31 / Protein transport protein SEC31 / Protein transport protein SEC31-like / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Ancestral coatomer element 1, Sec16/Sec31 / Sec16 Sec23-binding domain / Sec13/Seh1 family / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Protein transport protein SEC31 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 40 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 9, 2013Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Experimental preparation / Refinement description
Category: em_3d_fitting / em_sample_support / em_software
Item: _em_3d_fitting.target_criteria / _em_sample_support.grid_type ..._em_3d_fitting.target_criteria / _em_sample_support.grid_type / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.3Sep 11, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.4May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-2431
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Protein transport protein SEC31
B: Protein transport protein SEC13
C: Protein transport protein SEC31
F: Protein transport protein SEC13


Theoretical massNumber of molelcules
Total (without water)343,9414
Polymers343,9414
Non-polymers00
Water3,333185
1


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

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Components

#1: Protein Protein transport protein SEC31 / Protein WEB1


Mass: 138833.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC31, WEB1, YDL195W, D1229 / Plasmid: PNS3141 (6H31/CK1313) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY1112 / References: UniProt: P38968
#2: Protein Protein transport protein SEC13


Mass: 33082.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC13, ANU3, YLR208W, L8167.4 / Plasmid: PNS3141 (6H31/CK1313) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY1112 / References: UniProt: Q04491
#3: Protein Protein transport protein SEC13


Mass: 33191.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC13, ANU3, YLR208W, L8167.4 / Plasmid: PNS3141 (6H31/CK1313) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY1112 / References: UniProt: Q04491
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: SEC13/31 COMPLEX (AS PART OF COMPLETE COPII ASSEMBLED ON MEMBRANE) EDGE IN LEFT-HANDED DIRECTION
Type: COMPLEX
Buffer solutionName: HEPES, 50 MM KOAC, 1.2 MM MGCL2 / pH: 6.8 / Details: 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: C-FLAT GRIDS / Grid type: C-flat
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: ETHANE; HOMEMADE PLUNGER

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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 FIELD / 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
Radiation wavelengthRelative weight: 1

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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: C2 (2 fold cyclic)
3D reconstructionMethod: SUBTOMOGRAM ALIGNMENT AND AVERAGING / Resolution: 40 Å / Num. of particles: 192 / Nominal pixel size: 4.3 Å / Actual pixel size: 4.3 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2431. (DEPOSITION ID: 11863).
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 building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12PM6

2pm6

12PM61PDBexperimental model
22PM9

2pm9

12PM92PDBexperimental model
RefinementHighest resolution: 40 Å
Refinement stepCycle: LAST / Highest resolution: 40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15238 0 0 185 15423

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