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- PDB-7s16: Crystal structure of alpha-COP-WD40 domain R57A mutant -

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Basic information

Entry
Database: PDB / ID: 7s16
TitleCrystal structure of alpha-COP-WD40 domain R57A mutant
ComponentsCoatomer subunit alpha
KeywordsPROTEIN TRANSPORT / Coatomer subunit alpha WD40 R57A mutant
Function / homology
Function and homology information


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 / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity ...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 / cargo receptor activity / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / Golgi membrane / structural molecule activity / Golgi apparatus / cytoplasm
Similarity search - Function
: / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / Coatomer WD associated region / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. ...: / Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / Coatomer WD associated region / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Putative coatomer subunit alpha
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsDey, D. / Singh, S. / Khan, S. / Martin, M. / Schnicker, N. / Gakhar, L. / Pierce, B. / Hasan, S.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA134274 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA086862 United States
CitationJournal: Commun Biol / Year: 2022
Title: An extended motif in the SARS-CoV-2 spike modulates binding and release of host coatomer in retrograde trafficking
Authors: Dey, D. / Singh, S. / Khan, S. / Martin, M. / Schnicker, N.J. / Gakhar, L. / Pierce, B.G. / Hasan, S.S.
History
DepositionSep 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8352
Polymers38,8121
Non-polymers231
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.868, 56.712, 70.548
Angle α, β, γ (deg.)90.00, 99.37, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 38812.207 Da / Num. of mol.: 1 / Fragment: WD40 domain / Mutation: R57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Homo sapiens (human) / References: UniProt: Q96WV5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.82 Å3/Da / Density % sol: 32.54 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 3350 and 0.2M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.24→69.61 Å / Num. obs: 74665 / % possible obs: 94.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 14.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 5.4 / Net I/σ(I): 11.5
Reflection shellResolution: 1.24→1.26 Å / Num. unique obs: 2292 / CC1/2: 0.663

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J87

4j87


Resolution: 1.24→43.97 Å / SU ML: 0.101 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.74
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.159 3634 4.87 %
Rwork0.135 --
obs0.136 74567 94.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.78 Å2
Refinement stepCycle: LAST / Resolution: 1.24→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 1 343 2887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052696
X-RAY DIFFRACTIONf_angle_d0.913684
X-RAY DIFFRACTIONf_dihedral_angle_d11.638366
X-RAY DIFFRACTIONf_chiral_restr0.099402
X-RAY DIFFRACTIONf_plane_restr0.006467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.260.2853820.25281653X-RAY DIFFRACTION58
1.26-1.270.2602910.21951827X-RAY DIFFRACTION63
1.27-1.290.24561010.20812049X-RAY DIFFRACTION71
1.29-1.310.23631010.18132200X-RAY DIFFRACTION77
1.31-1.330.22551220.17522480X-RAY DIFFRACTION85
1.33-1.350.19051550.16172771X-RAY DIFFRACTION97
1.35-1.380.18791410.15212880X-RAY DIFFRACTION100
1.38-1.40.18481350.15072864X-RAY DIFFRACTION100
1.4-1.430.17341540.13272937X-RAY DIFFRACTION100
1.43-1.460.18281520.13282828X-RAY DIFFRACTION100
1.46-1.490.1781420.13152906X-RAY DIFFRACTION100
1.49-1.520.17221500.12412886X-RAY DIFFRACTION100
1.52-1.560.15381550.12012906X-RAY DIFFRACTION100
1.56-1.60.1431630.11712851X-RAY DIFFRACTION100
1.6-1.650.16271440.12282879X-RAY DIFFRACTION100
1.65-1.70.16271350.12812907X-RAY DIFFRACTION100
1.7-1.760.17821620.12912879X-RAY DIFFRACTION100
1.76-1.840.16531640.12952879X-RAY DIFFRACTION100
1.84-1.920.14431520.12622896X-RAY DIFFRACTION100
1.92-2.020.15671420.1262907X-RAY DIFFRACTION100
2.02-2.150.15891500.12722893X-RAY DIFFRACTION100
2.15-2.310.17641660.1312885X-RAY DIFFRACTION100
2.31-2.540.15661280.14782931X-RAY DIFFRACTION100
2.55-2.910.17661540.15172917X-RAY DIFFRACTION100
2.91-3.670.13711350.12682940X-RAY DIFFRACTION100
3.67-3.970.1321580.13112982X-RAY DIFFRACTION100

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