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- PDB-7s23: Crystal structure of alpha-COP-WD40 domain, Y139A mutant -

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Basic information

Entry
Database: PDB / ID: 7s23
TitleCrystal structure of alpha-COP-WD40 domain, Y139A mutant
ComponentsCoatomer subunit alpha
KeywordsPROTEIN TRANSPORT / Coatomer subunit alpha WD40 domain
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. ...: / 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: 1.49 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 3, 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
B: Coatomer subunit alpha
C: Coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)116,4193
Polymers116,4193
Non-polymers00
Water16,844935
1
A: Coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)38,8061
Polymers38,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)38,8061
Polymers38,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Coatomer subunit alpha


Theoretical massNumber of molelcules
Total (without water)38,8061
Polymers38,8061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.315, 171.553, 71.281
Angle α, β, γ (deg.)90.00, 99.71, 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: 38806.230 Da / Num. of mol.: 3 / Fragment: WD40 domain / Mutation: Y139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Homo sapiens (human) / References: UniProt: Q96WV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 935 / 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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 18% PEG3350 and 0.2M Potassium-sodium tartarate

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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: 1.49→171.55 Å / Num. obs: 140251 / % possible obs: 97.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Net I/σ(I): 5
Reflection shellResolution: 1.49→1.52 Å / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6840 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J87

4j87


Resolution: 1.49→65.02 Å / SU ML: 0.162 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.635
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.184 7007 5 %
Rwork0.14 --
obs0.142 140155 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.75 Å2
Refinement stepCycle: LAST / Resolution: 1.49→65.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7468 0 0 935 8403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057718
X-RAY DIFFRACTIONf_angle_d0.69610491
X-RAY DIFFRACTIONf_dihedral_angle_d14.712706
X-RAY DIFFRACTIONf_chiral_restr0.0861125
X-RAY DIFFRACTIONf_plane_restr0.0051327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.29392580.22844335X-RAY DIFFRACTION97
1.51-1.520.28062320.20894348X-RAY DIFFRACTION97
1.52-1.540.24982250.19094393X-RAY DIFFRACTION97
1.54-1.560.2462460.17924412X-RAY DIFFRACTION97
1.56-1.580.23022080.16394354X-RAY DIFFRACTION97
1.58-1.610.23382340.16084395X-RAY DIFFRACTION97
1.61-1.630.20392230.15154486X-RAY DIFFRACTION97
1.63-1.650.21562200.15064338X-RAY DIFFRACTION97
1.65-1.680.21272200.1494468X-RAY DIFFRACTION97
1.68-1.710.2252410.15144423X-RAY DIFFRACTION98
1.71-1.740.21422190.15574388X-RAY DIFFRACTION97
1.74-1.770.23752080.16244477X-RAY DIFFRACTION98
1.77-1.80.20972490.14574365X-RAY DIFFRACTION98
1.8-1.840.19562210.12334433X-RAY DIFFRACTION98
1.84-1.880.17622420.11974521X-RAY DIFFRACTION98
1.88-1.920.18212250.12444375X-RAY DIFFRACTION98
1.92-1.970.18242470.1164507X-RAY DIFFRACTION98
1.97-2.020.15732260.11964379X-RAY DIFFRACTION98
2.02-2.080.17622570.12454490X-RAY DIFFRACTION98
2.08-2.150.19392240.12764447X-RAY DIFFRACTION98
2.15-2.230.19122410.12124481X-RAY DIFFRACTION98
2.23-2.310.18132540.12844454X-RAY DIFFRACTION99
2.31-2.420.20112360.13744435X-RAY DIFFRACTION99
2.42-2.550.19112250.14574507X-RAY DIFFRACTION99
2.55-2.710.18932510.14774481X-RAY DIFFRACTION99
2.71-2.920.16162370.14264488X-RAY DIFFRACTION99
2.92-3.210.15482330.13734441X-RAY DIFFRACTION98
3.21-3.670.15952430.12954449X-RAY DIFFRACTION98
3.67-4.630.16252320.12524540X-RAY DIFFRACTION99
4.63-65.020.16872300.15914538X-RAY DIFFRACTION99

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