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- PDB-4j79: Crystal structure of beta'-COP/PEDVspike complex -

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Basic information

Entry
Database: PDB / ID: 4j79
TitleCrystal structure of beta'-COP/PEDVspike complex
Components
  • Coatomer subunit beta'
  • Spike glycoproteinSpike protein
KeywordsPROTEIN TRANSPORT / SEC27 / Beta propeller domain / ER retrieval signal
Function / homology
Function and homology information


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 / intracellular protein transport ...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 / intracellular protein transport / endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / Golgi membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / structural molecule activity / membrane
Similarity search - Function
Coatomer beta' subunit (COPB2) / Spike glycoprotein, Alphacoronavirus / Coatomer, WD associated region / Coatomer WD associated region / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller ...Coatomer beta' subunit (COPB2) / Spike glycoprotein, Alphacoronavirus / Coatomer, WD associated region / Coatomer WD associated region / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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 Beta
Similarity search - Domain/homology
Coatomer subunit beta' / Spike glycoprotein
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Porcine epidemic diarrhea virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.559 Å
AuthorsMa, W. / Goldberg, J.
CitationJournal: Embo J. / Year: 2013
Title: Rules for the recognition of dilysine retrieval motifs by coatomer.
Authors: Ma, W. / Goldberg, J.
History
DepositionFeb 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: Coatomer subunit beta'
B: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)35,0492
Polymers35,0492
Non-polymers00
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint1 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.100, 51.180, 85.250
Angle α, β, γ (deg.)90.00, 101.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-594-

HOH

31A-637-

HOH

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Components

#1: Protein Coatomer subunit beta' / / Beta'-coat protein / Beta'-COP


Mass: 34307.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P41811
#2: Protein/peptide Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


Mass: 740.846 Da / Num. of mol.: 1 / Fragment: UNP residues 1378-1383 / Source method: obtained synthetically / Source: (synth.) Porcine epidemic diarrhea virus / References: UniProt: Q91AV1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.29 Å3/Da / Density % sol: 46.25 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.559→83.465 Å / Num. obs: 43962 / % possible obs: 97.2 % / Observed criterion σ(I): 13.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.559→42.006 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1998 4.55 %RANDOM
Rwork0.1647 ---
obs0.1661 43890 96.74 %-
all-43962 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.559→42.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 0 358 2814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092525
X-RAY DIFFRACTIONf_angle_d1.3693444
X-RAY DIFFRACTIONf_dihedral_angle_d13.281894
X-RAY DIFFRACTIONf_chiral_restr0.103382
X-RAY DIFFRACTIONf_plane_restr0.006436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.559-1.59780.27511410.24732955X-RAY DIFFRACTION96
1.5978-1.6410.29631390.23962943X-RAY DIFFRACTION95
1.641-1.68930.27941410.23352947X-RAY DIFFRACTION95
1.6893-1.74380.30281400.22222929X-RAY DIFFRACTION95
1.7438-1.80610.28851390.21342929X-RAY DIFFRACTION96
1.8061-1.87840.21681420.20482949X-RAY DIFFRACTION95
1.8784-1.96390.24011410.18682957X-RAY DIFFRACTION96
1.9639-2.06750.19841410.16982980X-RAY DIFFRACTION96
2.0675-2.1970.21331450.16213019X-RAY DIFFRACTION99
2.197-2.36660.19791460.16383060X-RAY DIFFRACTION99
2.3666-2.60470.22271430.16633002X-RAY DIFFRACTION98
2.6047-2.98160.18811460.15883071X-RAY DIFFRACTION99
2.9816-3.75610.16291460.14243053X-RAY DIFFRACTION98
3.7561-42.0210.15041480.14433098X-RAY DIFFRACTION97

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