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- PDB-3mkr: Crystal structure of yeast alpha/epsilon-COP subcomplex of the CO... -

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Basic information

Entry
Database: PDB / ID: 3mkr
TitleCrystal structure of yeast alpha/epsilon-COP subcomplex of the COPI vesicular coat
Components
  • Coatomer subunit alpha
  • Coatomer subunit epsilon
KeywordsTRANSPORT PROTEIN / tetratricopeptide repeats (TPR) / beta-hairpin / alpha-solenoid
Function / homology
Function and homology information


protein localization to axon / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / hormone activity / protein transport ...protein localization to axon / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / COPI vesicle coat / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / hormone activity / protein transport / Golgi membrane / structural molecule activity / extracellular region / nucleoplasm
Similarity search - Function
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 / : / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat domain ...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 / : / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / 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 alpha / Coatomer subunit epsilon
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsLee, C. / Goldberg, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Structure of coatomer cage proteins and the relationship among COPI, COPII, and clathrin vesicle coats.
Authors: Lee, C. / Goldberg, J.
History
DepositionApr 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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 epsilon
B: Coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)69,4222
Polymers69,4222
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-42 kcal/mol
Surface area28280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.629, 176.629, 141.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Coatomer subunit epsilon / / Epsilon-coat protein / Epsilon-COP


Mass: 33108.453 Da / Num. of mol.: 1 / Fragment: UNP Residues 17-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COPE, COPE1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q28104
#2: Protein Coatomer subunit alpha / / Alpha-coat protein / Alpha-COP / HEP-COP / HEPCOP / Renin / Xenopsin-related peptide / Prorenin


Mass: 36313.223 Da / Num. of mol.: 1 / Fragment: UNP Residues 905-1224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: COPA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q27954
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 68.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 11% PEG 4000, 0.1M sodium citrate, 5mM DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.9792, 0.9794, 0.9642
SYNCHROTRONNSLS X2520.9794
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDAug 24, 2006
ADSC QUANTUM 42CCDJul 28, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.96421
ReflectionResolution: 2.6→50 Å / Num. obs: 34363 / % possible obs: 99.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.042 / Net I/σ(I): 28.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3345 / Rsym value: 0.334 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.6→29.84 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 143691.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1625 4.9 %RANDOM
Rwork0.222 ---
obs0.222 32909 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.3861 Å2 / ksol: 0.343375 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.9 Å20 Å20 Å2
2--8.22 Å20 Å2
3----14.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4874 0 0 34 4908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 246 5 %
Rwork0.342 4704 -
obs--87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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