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- PDB-3mv2: Crystal Structure of a-COP in Complex with e-COP -

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Basic information

Entry
Database: PDB / ID: 3mv2
TitleCrystal Structure of a-COP in Complex with e-COP
Components
  • Coatomer subunit alpha
  • Coatomer subunit epsilon
KeywordsPROTEIN TRANSPORT / Vesicular Membrane Coat Coat Protein Complex I
Function / homology
Function and homology information


vesicle coating / COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / intracellular mRNA localization / late endosome to vacuole transport via multivesicular body sorting pathway / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding ...vesicle coating / COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / intracellular mRNA localization / late endosome to vacuole transport via multivesicular body sorting pathway / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin binding / promoter-specific chromatin binding / intracellular protein transport / protein transport / Golgi membrane / structural molecule activity
Similarity search - Function
Coatomer epsilon subunit / Coatomer, epsilon subunit / : / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / Coatomer WD associated region / Quinoprotein amine dehydrogenase, beta chain-like / Tetratricopeptide repeat domain ...Coatomer epsilon subunit / Coatomer, epsilon subunit / : / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / Coatomer WD associated region / Quinoprotein amine dehydrogenase, beta chain-like / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / 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 / Mainly Alpha
Similarity search - Domain/homology
Coatomer subunit epsilon / Coatomer subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsHoelz, A. / Hsia, K.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Crystal structure of alpha-COP in complex with epsilon-COP provides insight into the architecture of the COPI vesicular coat.
Authors: Hsia, K.C. / Hoelz, A.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coatomer subunit alpha
B: Coatomer subunit epsilon
C: Coatomer subunit alpha
D: Coatomer subunit epsilon
E: Coatomer subunit alpha
F: Coatomer subunit epsilon


Theoretical massNumber of molelcules
Total (without water)215,7136
Polymers215,7136
Non-polymers00
Water0
1
A: Coatomer subunit alpha
B: Coatomer subunit epsilon


Theoretical massNumber of molelcules
Total (without water)71,9042
Polymers71,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-29 kcal/mol
Surface area26900 Å2
MethodPISA
2
C: Coatomer subunit alpha
D: Coatomer subunit epsilon


Theoretical massNumber of molelcules
Total (without water)71,9042
Polymers71,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-27 kcal/mol
Surface area26800 Å2
MethodPISA
3
E: Coatomer subunit alpha
F: Coatomer subunit epsilon


Theoretical massNumber of molelcules
Total (without water)71,9042
Polymers71,9042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-28 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)329.127, 74.382, 97.247
Angle α, β, γ (deg.)90.000, 102.270, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Coatomer subunit alpha / / Alpha-coat protein / Alpha-COP


Mass: 36429.906 Da / Num. of mol.: 3 / Fragment: UNP residues 891-1192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: COP1, D1578, RET1, SEC33, YDL145C / Production host: Escherichia coli (E. coli) / References: UniProt: P53622
#2: Protein Coatomer subunit epsilon / / Epsilon-coat protein / Epsilon-COP


Mass: 35474.449 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC28, YIL076W / Production host: Escherichia coli (E. coli) / References: UniProt: P40509

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 100 mM HEPES, pH. 7.2 200 mM ammonium citrate 18 (w/v) % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03316 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 51235 / % possible obs: 93.3 % / Redundancy: 3.1 % / Rsym value: 0.102
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.368

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.297 1938 3.8 %
Rwork0.246 --
obs-43769 85.4 %
Solvent computationBsol: 70.006 Å2
Displacement parametersBiso max: 203.72 Å2 / Biso mean: 125.898 Å2 / Biso min: 31.04 Å2
Baniso -1Baniso -2Baniso -3
1--34.93 Å20 Å2-23.096 Å2
2--28.307 Å20 Å2
3---6.623 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14273 0 0 0 14273
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.64
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:protein_rep.param

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