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- PDB-8pxj: Structure of Whitewater Arroyo virus GP1 glycoprotein, solved at ... -

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Basic information

Entry
Database: PDB / ID: 8pxj
TitleStructure of Whitewater Arroyo virus GP1 glycoprotein, solved at wavelength 2.75 A
ComponentsGlycoprotein G1
KeywordsVIRAL PROTEIN / glycoprotein
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
: / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMammarenavirus whitewaterense
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsEl Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C. / Bowden, T.A. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoprotein G1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,18212
Polymers18,6521
Non-polymers1,53011
Water00
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)106.830, 106.830, 74.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-309-

CD

21A-311-

SO4

31A-311-

SO4

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Components

#1: Protein Glycoprotein G1 / GP1


Mass: 18652.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammarenavirus whitewaterense / Gene: GPC, GP-C / Production host: Homo sapiens (human) / References: UniProt: Q911P0
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
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: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.0 mg/ml protein, 0.1 M HEPES-Na pH 7.5, and 0.05 M cadmium sulphate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.7552 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jul 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.7552 Å / Relative weight: 1
ReflectionResolution: 2.75→46.3 Å / Num. obs: 6783 / % possible obs: 97.2 % / Redundancy: 30.7 % / Biso Wilson estimate: 102.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1404 / Rpim(I) all: 0.02522 / Rrim(I) all: 0.1428 / Net I/σ(I): 21.54
Reflection shellResolution: 2.75→2.848 Å / Mean I/σ(I) obs: 0.88 / Num. unique obs: 608 / CC1/2: 0.567

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→46.3 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.932 / SU B: 45.082 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R: 0.622 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27618 352 5.2 %RANDOM
Rwork0.2492 ---
obs0.25059 6431 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 117.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å21.15 Å20 Å2
2--2.3 Å2-0 Å2
3----7.45 Å2
Refinement stepCycle: 1 / Resolution: 2.75→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 58 0 1218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121252
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161129
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.6621702
X-RAY DIFFRACTIONr_angle_other_deg0.3791.582601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6985145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.75754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24910196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.050.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021413
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02282
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.0898.272583
X-RAY DIFFRACTIONr_mcbond_other7.088.275583
X-RAY DIFFRACTIONr_mcangle_it10.55214.872727
X-RAY DIFFRACTIONr_mcangle_other10.54814.877728
X-RAY DIFFRACTIONr_scbond_it8.3278.987669
X-RAY DIFFRACTIONr_scbond_other8.2398.93662
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.23816.114964
X-RAY DIFFRACTIONr_long_range_B_refined17.536101.85082
X-RAY DIFFRACTIONr_long_range_B_other17.534101.85083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.531 12 -
Rwork0.476 441 -
obs--91.15 %
Refinement TLS params.Method: refined / Origin x: 43.7699 Å / Origin y: 13.5606 Å / Origin z: -5.7353 Å
111213212223313233
T0.231 Å2-0.0694 Å20.0264 Å2-0.0834 Å20.1078 Å2--0.2354 Å2
L4.5061 °21.8375 °21.7515 °2-5.1688 °20.6067 °2--6.0141 °2
S0.1259 Å °-0.3789 Å °-0.4576 Å °0.492 Å °0.0105 Å °0.3912 Å °1.0083 Å °-0.4938 Å °-0.1364 Å °

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