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Open data
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Basic information
Entry | Database: PDB / ID: 5a1y | ||||||
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Title | The structure of the COPI coat linkage IV | ||||||
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![]() | TRANSPORT PROTEIN / COPI / COATOMER / COATED VESICLES | ||||||
Function / homology | ![]() cerebellar Purkinje cell layer maturation / protein localization to cell leading edge / Synthesis of PIPs at the plasma membrane / protein localization to axon / VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / protein localization to Golgi membrane / Golgi localization ...cerebellar Purkinje cell layer maturation / protein localization to cell leading edge / Synthesis of PIPs at the plasma membrane / protein localization to axon / VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / protein localization to Golgi membrane / Golgi localization / COPI-coated vesicle / pancreatic juice secretion / organelle membrane contact site / regulation of Golgi organization / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI-mediated anterograde transport / COPI vesicle coat / positive regulation of mitochondrial fusion / Golgi vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / organelle transport along microtubule / regulation of fatty acid metabolic process / establishment of Golgi localization / Golgi to plasma membrane transport / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Golgi-associated vesicle / pigmentation / positive regulation of mitochondrial fission / endoplasmic reticulum-Golgi intermediate compartment / protein secretion / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / Neutrophil degranulation / adult locomotory behavior / small monomeric GTPase / establishment of localization in cell / macroautophagy / protein kinase C binding / intracellular protein transport / hormone activity / protein transport / growth cone / Golgi membrane / axon / GTPase activity / mRNA binding / neuronal cell body / GTP binding / structural molecule activity / Golgi apparatus / endoplasmic reticulum / extracellular space / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 21 Å | ||||||
![]() | Dodonova, S.O. / Diestelkoetter-Bachert, P. / von Appen, A. / Hagen, W.J.H. / Beck, R. / Beck, M. / Wieland, F. / Briggs, J.A.G. | ||||||
![]() | ![]() Title: VESICULAR TRANSPORT. A structure of the COPI coat and the role of coat proteins in membrane vesicle assembly. Authors: S O Dodonova / P Diestelkoetter-Bachert / A von Appen / W J H Hagen / R Beck / M Beck / F Wieland / J A G Briggs / ![]() Abstract: Transport of material within cells is mediated by trafficking vesicles that bud from one cellular compartment and fuse with another. Formation of a trafficking vesicle is driven by membrane coats ...Transport of material within cells is mediated by trafficking vesicles that bud from one cellular compartment and fuse with another. Formation of a trafficking vesicle is driven by membrane coats that localize cargo and polymerize into cages to bend the membrane. Although extensive structural information is available for components of these coats, the heterogeneity of trafficking vesicles has prevented an understanding of how complete membrane coats assemble on the membrane. We combined cryo-electron tomography, subtomogram averaging, and cross-linking mass spectrometry to derive a complete model of the assembled coat protein complex I (COPI) coat involved in traffic between the Golgi and the endoplasmic reticulum. The highly interconnected COPI coat structure contradicted the current "adaptor-and-cage" understanding of coated vesicle formation. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 1.2 MB | Display | ![]() |
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PDB format | ![]() | 761.7 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 785.3 KB | Display | ![]() |
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Full document | ![]() | 841.5 KB | Display | |
Data in XML | ![]() | 187.9 KB | Display | |
Data in CIF | ![]() | 328.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2989MC ![]() 2985C ![]() 2986C ![]() 2987C ![]() 2988C ![]() 5a1uC ![]() 5a1vC ![]() 5a1wC ![]() 5a1xC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Protein , 1 types, 5 molecules ABIJR
#1: Protein | Mass: 20552.438 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: POW12 / Production host: ![]() ![]() |
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-COATOMER SUBUNIT ... , 7 types, 16 molecules CKDLEMVFNWGOHPXZ
#2: Protein | Mass: 142532.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 102566.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 97622.703 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #5: Protein | Mass: 20218.168 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #6: Protein | Mass: 109148.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #7: Protein | Mass: 57304.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #8: Protein | Mass: 34605.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: electron tomography |
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Sample preparation
Component | Name: COPI COAT LINKAGE IV ON THE MEMBRANE / Type: ORGANELLE OR CELLULAR COMPONENT |
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Buffer solution | Name: 50 MM HEPES, 50 MM KAC, 1MM MGCL2 / pH: 7.4 / Details: 50 MM HEPES, 50 MM KAC, 1MM MGCL2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Feb 7, 2014 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 42000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm |
Specimen holder | Temperature: 90 K / Tilt angle max: 60 ° / Tilt angle min: -45 ° |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN MULTISCAN |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: PHASE FLIPPING OF INDIVIDUAL TILTS | ||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||
3D reconstruction | Method: CROSS-CORRELATION / Resolution: 21 Å / Num. of particles: 1205 / Nominal pixel size: 2.019 Å Details: HOMOLOGY MODELS WERE FITTED INTO THE EM MAP USING THE MDFF (MOLECULAR DYNAMICS FLEXIBLE FITTING) SOFTWARE. DUE TO LOW RESOLUTION OF THE EM MAP USED FOR FITTING, WE DEPOSIT ONLY THE BACKBONE ...Details: HOMOLOGY MODELS WERE FITTED INTO THE EM MAP USING THE MDFF (MOLECULAR DYNAMICS FLEXIBLE FITTING) SOFTWARE. DUE TO LOW RESOLUTION OF THE EM MAP USED FOR FITTING, WE DEPOSIT ONLY THE BACKBONE ATOMS. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2989. (DEPOSITION ID: 13343). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--HOMOLOGY-MODEL | ||||||||||||
Refinement | Highest resolution: 21 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 21 Å
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