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- PDB-8enz: Crystal structure of alpha-COPI-WD40 domain K15A mutant. -

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Basic information

Entry
Database: PDB / ID: 8enz
TitleCrystal structure of alpha-COPI-WD40 domain K15A mutant.
ComponentsPutative coatomer subunit alpha
KeywordsPROTEIN TRANSPORT / COPI / protein trafficking / SARS-CoV-2 spike / dibasic motif
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
ACETYL GROUP / Putative coatomer subunit alpha
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsDey, D. / 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 Institute of General Medical Sciences (NIH/NIGMS)R01GM150187 United States
CitationJournal: Nat Commun / Year: 2023
Title: A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs.
Authors: Dey, D. / Qing, E. / He, Y. / Chen, Y. / Jennings, B. / Cohn, W. / Singh, S. / Gakhar, L. / Schnicker, N.J. / Pierce, B.G. / Whitelegge, J.P. / Doray, B. / Orban, J. / Gallagher, T. / Hasan, S.S.
History
DepositionSep 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative coatomer subunit alpha
B: Putative coatomer subunit alpha
C: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,5756
Polymers116,4433
Non-polymers1323
Water13,241735
1
A: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8582
Polymers38,8141
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8582
Polymers38,8141
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative coatomer subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8582
Polymers38,8141
Non-polymers441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.487, 172.265, 71.483
Angle α, β, γ (deg.)90.000, 99.910, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 38814.184 Da / Num. of mol.: 3 / Mutation: K15A
Source method: isolated from a genetically manipulated source
Details: Fo-Fc electron density for 172-199 and 332-337 not detected.
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Homo sapiens (human) / References: UniProt: Q96WV5
#2: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.91 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.14M Sodium citrate tribasic dihydrate, 18% PEG3350

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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 9M / Detector: PIXEL / Date: Jun 26, 2022 / Details: KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.65→28.84 Å / Num. obs: 105146 / % possible obs: 98.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.68 Å2 / CC1/2: 0.995 / Rsym value: 0.07 / Net I/σ(I): 8.4
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 10362 / CC1/2: 0.805 / Rsym value: 0.445 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.65→28.71 Å / SU ML: 0.162 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.9861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1934 10203 4.98 %
Rwork0.163 194499 -
obs0.1645 204702 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.37 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7464 0 9 735 8208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01447708
X-RAY DIFFRACTIONf_angle_d1.229810473
X-RAY DIFFRACTIONf_chiral_restr0.08081116
X-RAY DIFFRACTIONf_plane_restr0.01391326
X-RAY DIFFRACTIONf_dihedral_angle_d7.51291004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.27373540.25666363X-RAY DIFFRACTION96.25
1.67-1.690.25763440.24746511X-RAY DIFFRACTION95.74
1.69-1.710.26032730.23976487X-RAY DIFFRACTION95.04
1.71-1.730.29833320.22836510X-RAY DIFFRACTION98.29
1.73-1.750.28433930.22066498X-RAY DIFFRACTION97.06
1.75-1.780.23783900.21086460X-RAY DIFFRACTION95.22
1.78-1.80.26793180.20736449X-RAY DIFFRACTION97.07
1.8-1.830.23763850.19826451X-RAY DIFFRACTION97.56
1.83-1.860.21893330.1896539X-RAY DIFFRACTION96.56
1.86-1.890.1993410.18116509X-RAY DIFFRACTION96.26
1.89-1.920.25233090.18076549X-RAY DIFFRACTION97.73
1.92-1.960.23163560.16996474X-RAY DIFFRACTION96.32
1.96-1.990.20033280.17036423X-RAY DIFFRACTION95.75
1.99-2.030.21043480.16396246X-RAY DIFFRACTION94.09
2.03-2.080.2083510.16936348X-RAY DIFFRACTION92.98
2.08-2.130.21143400.16026441X-RAY DIFFRACTION98.25
2.13-2.180.18783450.15936603X-RAY DIFFRACTION97.54
2.18-2.240.20583740.15926360X-RAY DIFFRACTION94.85
2.24-2.310.20072910.15746304X-RAY DIFFRACTION93.67
2.31-2.380.20233280.15476587X-RAY DIFFRACTION97.82
2.38-2.460.18853780.16716589X-RAY DIFFRACTION98.47
2.46-2.560.2173470.15926527X-RAY DIFFRACTION98.07
2.56-2.680.2223020.16176703X-RAY DIFFRACTION97.92
2.68-2.820.19863170.15376583X-RAY DIFFRACTION98.61
2.82-30.19133620.15676543X-RAY DIFFRACTION97.98
3-3.230.16433040.14956665X-RAY DIFFRACTION98.56
3.23-3.550.16222840.1456568X-RAY DIFFRACTION96.75
3.55-4.070.16823660.14186301X-RAY DIFFRACTION94.03
4.07-5.120.12793360.12496330X-RAY DIFFRACTION94.42
5.12-28.710.19593740.18566578X-RAY DIFFRACTION98.33

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