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- PDB-5a1y: The structure of the COPI coat linkage IV -

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Basic information

Entry
Database: PDB / ID: 5a1y
TitleThe structure of the COPI coat linkage IV
Components
  • (COATOMER SUBUNIT ...) x 7
  • ADP-RIBOSYLATION FACTOR 1ARF1
KeywordsTRANSPORT PROTEIN / COPI / COATOMER / COATED VESICLES
Function / homology
Function and homology information


cerebellar Purkinje cell layer maturation / protein localization to cell leading edge / protein localization to axon / VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Golgi localization / COPI-coated vesicle / pancreatic juice secretion ...cerebellar Purkinje cell layer maturation / protein localization to cell leading edge / protein localization to axon / VxPx cargo-targeting to cilium / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Golgi localization / COPI-coated vesicle / pancreatic juice secretion / COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI-mediated anterograde transport / Golgi vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / organelle transport along microtubule / intra-Golgi vesicle-mediated transport / Golgi to plasma membrane transport / establishment of Golgi localization / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / pigmentation / Golgi-associated vesicle / protein secretion / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / Neutrophil degranulation / adult locomotory behavior / small monomeric GTPase / protein kinase C binding / establishment of localization in cell / macroautophagy / intracellular protein transport / hormone activity / protein transport / growth cone / axon / Golgi membrane / mRNA binding / intracellular membrane-bounded organelle / GTPase activity / neuronal cell body / structural molecule activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular space / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Coatomer epsilon subunit / Coatomer, epsilon subunit / Coatomer beta subunit, C-terminal / Coatomer beta subunit (COPB1) / Coatomer beta subunit, appendage platform domain / Coatomer beta C-terminal region / Coatomer beta subunit appendage platform / Coatomer, gamma subunit, appendage, Ig-like subdomain / Coatomer gamma subunit / Coatomer subunit gamma, C-terminal ...Coatomer epsilon subunit / Coatomer, epsilon subunit / Coatomer beta subunit, C-terminal / Coatomer beta subunit (COPB1) / Coatomer beta subunit, appendage platform domain / Coatomer beta C-terminal region / Coatomer beta subunit appendage platform / Coatomer, gamma subunit, appendage, Ig-like subdomain / Coatomer gamma subunit / Coatomer subunit gamma, C-terminal / Coatomer, gamma subunit, appendage domain superfamily / Coatomer subunit zeta / Coatomer gamma subunit appendage platform subdomain / Coatomer subunit gamma-1 C-terminal appendage platform / Coatomer delta subunit / : / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / Coatomer (COPI) alpha subunit C-terminus / Coatomer beta' subunit (COPB2) / Coatomer, WD associated region / Coatomer WD associated region / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / ADP-ribosylation factor 1-5 / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / small GTPase Arf family profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Longin-like domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / Anaphase-promoting complex subunit 4 WD40 domain / TBP domain superfamily / Rab subfamily of small GTPases / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Small GTP-binding protein domain / Armadillo-type fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Coatomer subunit beta' / Coatomer subunit epsilon / ADP-ribosylation factor 1 / Coatomer subunit zeta-1 / Coatomer subunit delta / Coatomer subunit alpha / Coatomer subunit beta / Coatomer subunit gamma-1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MUS MUSCULUS (house mouse)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 21 Å
AuthorsDodonova, S.O. / Diestelkoetter-Bachert, P. / von Appen, A. / Hagen, W.J.H. / Beck, R. / Beck, M. / Wieland, F. / Briggs, J.A.G.
CitationJournal: Science / Year: 2015
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.
History
DepositionMay 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references / Other
Revision 1.2Aug 23, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_image_scans / em_software
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

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-2989
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  • Imaged by UCSF Chimera
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Assembly

Deposited unit
A: ADP-RIBOSYLATION FACTOR 1
B: ADP-RIBOSYLATION FACTOR 1
C: COATOMER SUBUNIT ALPHA
D: COATOMER SUBUNIT BETA'
E: COATOMER SUBUNIT GAMMA-1
F: COATOMER SUBUNIT ZETA-1
G: COATOMER SUBUNIT BETA
H: COATOMER SUBUNIT DELTA
I: ADP-RIBOSYLATION FACTOR 1
J: ADP-RIBOSYLATION FACTOR 1
K: COATOMER SUBUNIT ALPHA
L: COATOMER SUBUNIT BETA'
M: COATOMER SUBUNIT GAMMA-1
N: COATOMER SUBUNIT ZETA-1
O: COATOMER SUBUNIT BETA
P: COATOMER SUBUNIT DELTA
R: ADP-RIBOSYLATION FACTOR 1
V: COATOMER SUBUNIT GAMMA-1
W: COATOMER SUBUNIT ZETA-1
X: COATOMER SUBUNIT EPSILON
Z: COATOMER SUBUNIT EPSILON


Theoretical massNumber of molelcules
Total (without water)1,348,59721
Polymers1,348,59721
Non-polymers00
Water0
1


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

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Components

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Protein , 1 types, 5 molecules ABIJR

#1: Protein
ADP-RIBOSYLATION FACTOR 1 / ARF1


Mass: 20552.438 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: POW12 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P11076

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COATOMER SUBUNIT ... , 7 types, 16 molecules CKDLEMVFNWGOHPXZ

#2: Protein COATOMER SUBUNIT ALPHA / / ALPHA-COAT PROTEIN / ALPHA-COP / XENOPSIN-RELATED PEPTIDE


Mass: 142532.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFBDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8CIE6
#3: Protein COATOMER SUBUNIT BETA' / / "BETA-COAT PROTEIN" / "BETA-COP" / P102


Mass: 102566.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFBDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O55029
#4: Protein COATOMER SUBUNIT GAMMA-1 / / GAMMA-1-COAT PROTEIN / GAMMA-1-COP


Mass: 97622.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFBDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9QZE5
#5: Protein COATOMER SUBUNIT ZETA-1 / / ZETA-1-COAT PROTEIN / ZETA-1 COP


Mass: 20218.168 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFBDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P61924
#6: Protein COATOMER SUBUNIT BETA / / BETA-COAT PROTEIN / BETA-COP


Mass: 109148.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFBDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9JIF7
#7: Protein COATOMER SUBUNIT DELTA / / ARCHAIN / DELTA-COAT PROTEIN / DELTA-COP


Mass: 57304.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFBDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q5XJY5
#8: Protein COATOMER SUBUNIT EPSILON / / EPSILON-COAT PROTEIN / EPSILON-COP


Mass: 34605.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFBDM / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O89079

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: COPI COAT LINKAGE IV ON THE MEMBRANE / Type: ORGANELLE OR CELLULAR COMPONENT
Buffer solutionName: 50 MM HEPES, 50 MM KAC, 1MM MGCL2 / pH: 7.4 / Details: 50 MM HEPES, 50 MM KAC, 1MM MGCL2
SpecimenEmbedding 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: Feb 7, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 42000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderTemperature: 90 K / Tilt angle max: 60 ° / Tilt angle min: -45 °
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN MULTISCAN
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2AV33D reconstruction
3TOM Toolbox3D reconstruction
CTF correctionDetails: PHASE FLIPPING OF INDIVIDUAL TILTS
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: 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 buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--HOMOLOGY-MODEL
RefinementHighest resolution: 21 Å
Refinement stepCycle: LAST / Highest resolution: 21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39957 0 0 0 39957

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