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- PDB-9dzx: MHV spike tail heptapeptide complexed with coatomer alpha-WD40 domain -

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Basic information

Entry
Database: PDB / ID: 9dzx
TitleMHV spike tail heptapeptide complexed with coatomer alpha-WD40 domain
Components
  • Putative coatomer subunit alpha
  • SER-HIS-GLU-ASP
KeywordsPROTEIN TRANSPORT
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 / : / : / COPA/B second beta-propeller / COPA/B TPR domain / WD domain, G-beta repeat ...Coatomer, alpha subunit, C-terminal / Coatomer subunit alpha / : / Coatomer (COPI) alpha subunit C-terminus / Coatomer, WD associated region / : / : / COPA/B second beta-propeller / COPA/B TPR domain / WD domain, G-beta repeat / 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. / 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)
Murine hepatitis virus strain A59
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsShakya, A.K. / Hasan, S.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: MHV spike tail heptapeptide complexed with coatomer alpha-WD40 domain
Authors: Shakya, A.K. / Hasan, S.S.
History
DepositionOct 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative coatomer subunit alpha
B: SER-HIS-GLU-ASP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,86416
Polymers51,9652
Non-polymers89914
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.118, 75.126, 129.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 51162.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: SPBPJ4664.04 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96WV5
#2: Protein/peptide SER-HIS-GLU-ASP


Mass: 801.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Murine hepatitis virus strain A59
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.78 Å3/Da / Density % sol: 30.97 % / Description: Rod shape
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 10% PEG 8000, 8% Ethylene Glycol

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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: 0.92011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 13, 2024 / Details: KB bimorph mirrors
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92011 Å / Relative weight: 1
ReflectionResolution: 1.66→33.99 Å / Num. obs: 44353 / % possible obs: 99.21 % / Redundancy: 2 % / Biso Wilson estimate: 22.51 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.046 / Rrim(I) all: 0.135 / Net I/σ(I): 9.6
Reflection shellResolution: 1.66→1.66 Å / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 9.6 / Num. unique obs: 44487 / CC1/2: 0.998 / Rpim(I) all: 0.026 / Rrim(I) all: 0.055 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487+SVNrefinement
PHENIX1.20.1_4487+SVNrefinement
HKL-3000data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→33.99 Å / SU ML: 0.2382 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2075 2216 5 %
Rwork0.1764 42133 -
obs0.1779 44349 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.4 Å2
Refinement stepCycle: LAST / Resolution: 1.66→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 58 227 2774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652606
X-RAY DIFFRACTIONf_angle_d0.95043512
X-RAY DIFFRACTIONf_chiral_restr0.0651373
X-RAY DIFFRACTIONf_plane_restr0.0077443
X-RAY DIFFRACTIONf_dihedral_angle_d8.6658348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.38681300.38682387X-RAY DIFFRACTION92.06
1.7-1.740.38261430.33772515X-RAY DIFFRACTION96.9
1.74-1.780.30831440.292568X-RAY DIFFRACTION98.55
1.78-1.830.28571310.23752633X-RAY DIFFRACTION99.78
1.83-1.880.28691450.21132596X-RAY DIFFRACTION100
1.88-1.940.23251360.19552609X-RAY DIFFRACTION99.93
1.94-2.010.22391440.19382641X-RAY DIFFRACTION100
2.01-2.090.26031350.19992620X-RAY DIFFRACTION100
2.09-2.190.2261070.17092658X-RAY DIFFRACTION99.96
2.19-2.30.20061330.16832647X-RAY DIFFRACTION100
2.3-2.450.2211380.17072648X-RAY DIFFRACTION100
2.45-2.640.21751600.17362646X-RAY DIFFRACTION100
2.64-2.90.18341280.16842691X-RAY DIFFRACTION100
2.9-3.320.18451430.15542685X-RAY DIFFRACTION100
3.32-4.180.15961450.14512740X-RAY DIFFRACTION100
4.19-33.990.18671540.16222849X-RAY DIFFRACTION99.97

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