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- PDB-8ofn: Structure of the yellow fever virus (Asibi strain) dimeric envelo... -

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Basic information

Entry
Database: PDB / ID: 8ofn
TitleStructure of the yellow fever virus (Asibi strain) dimeric envelope protein
ComponentsEnvelope glycoprotein
KeywordsVIRAL PROTEIN / YELLOW FEVER ENVELOPE PROTEIN / ASIBI STRAIN
Function / homology
Function and homology information


host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily ...Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesYellow fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.48 Å
AuthorsCovernton, E. / Vaney, M.C. / Barba-Spaeth, G. / Rey, F.A.
Funding support France, 1items
OrganizationGrant numberCountry
Pasteur Institute France
CitationJournal: Mbio / Year: 2023
Title: New insight into flavivirus maturation from structure/function studies of the yellow fever virus envelope protein complex.
Authors: Crampon, E. / Covernton, E. / Vaney, M.C. / Dellarole, M. / Sommer, S. / Sharma, A. / Haouz, A. / England, P. / Lepault, J. / Duquerroy, S. / Rey, F.A. / Barba-Spaeth, G.
History
DepositionMar 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3558
Polymers92,7782
Non-polymers5766
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: The biological assembly is the dimeric envelope E protein as it is on the virus. The final structure showed two independent molecules in the crystal asymmetric unit, generating the ...Evidence: The biological assembly is the dimeric envelope E protein as it is on the virus. The final structure showed two independent molecules in the crystal asymmetric unit, generating the classical head-to tail sE dimer through a 2-fold crystallographic symmetry axis.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-70 kcal/mol
Surface area38660 Å2
Unit cell
Length a, b, c (Å)92.540, 92.540, 308.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Envelope glycoprotein


Mass: 46389.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The E protein sequence contains residues from 1 to 392. After the last residue E392 of the protein seen in density, there are residues : G is a linker LVPRGS is the sequence of the thrombin ...Details: The E protein sequence contains residues from 1 to 392. After the last residue E392 of the protein seen in density, there are residues : G is a linker LVPRGS is the sequence of the thrombin cleavage site SAWSHPQFEKGGSGGGSGGSAWSHPQFEK is the double-strep-tag
Source: (gene. exp.) Yellow fever virus / Strain: ASIBI / Cell line (production host): SCHNEIDER S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: D0VF48
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.26M ammonium sulfate, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2018
RadiationMonochromator: channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.48→46.3 Å / Num. obs: 17868 / % possible obs: 93.4 % / Redundancy: 15.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.03 / Rrim(I) all: 0.121 / Net I/σ(I): 13.1
Reflection shellResolution: 3.48→3.81 Å / Rmerge(I) obs: 2.2 / Num. unique obs: 568 / CC1/2: 0.66 / Rpim(I) all: 0.6 / Rrim(I) all: 2.28

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Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.48→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.786
RfactorNum. reflection% reflectionSelection details
Rfree0.273 983 8.46 %RANDOM
Rwork0.255 ---
obs0.256 11613 64.3 %-
Displacement parametersBiso mean: 169.69 Å2
Baniso -1Baniso -2Baniso -3
1--3.1469 Å20 Å20 Å2
2---3.1469 Å20 Å2
3---6.2939 Å2
Refine analyzeLuzzati coordinate error obs: 0.7 Å
Refinement stepCycle: 1 / Resolution: 3.48→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 30 0 5964
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0066086HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.868268HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2080SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes154HARMONIC2
X-RAY DIFFRACTIONt_gen_planes872HARMONIC5
X-RAY DIFFRACTIONt_it6086HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion15.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion818SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6468SEMIHARMONIC4
LS refinement shellResolution: 3.48→3.81 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3896 -6.48 %
Rwork0.2909 664 -
all0.2975 710 -
obs--16.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.17590.18572.91045.8385-0.39265.30820.0150.184-0.5442-0.54420.03860.54420.46340.3815-0.05360.177-0.152-0.152-0.25970.152-0.042-5.6887-8.9906-35.1279
21.1430.09632.91048.3154-1.50541.47110.13340.1541-0.348-0.0295-0.30120.19310.1214-0.01670.16780.304-0.152-0.152-0.02320.152-0.304-22.417829.2567-59.2993
38.3154-2.47552.08968.3154-2.91048.3155-0.2190.5442-0.5442-0.26550.1446-0.5442-0.00930.54420.0744-0.3037-0.05070.01340.02090.152-0.059912.9086-12.6329-16.4574
42.0965-0.15642.91048.31540.00055.35340.04110.16540.4269-0.3632-0.50310.4165-0.37910.54420.4620.20560.152-0.152-0.29720.152-0.1525-19.51824.5059-21.2305
52.96812.91042.91047.96981.92110.8207-0.1530.4330.29270.2655-0.06930.5442-0.2289-0.20440.22230.28770.152-0.152-0.0589-0.152-0.2853-44.0606-13.5379-38.7402
66.22712.9092.6748.3127-2.28388.31550.0659-0.45670.54420.0541-0.1958-0.5442-0.54420.54420.12990.3040.0218-0.152-0.3040.152-0.2033-0.784727.2941-2.4107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1-53 }A1 - 53
2X-RAY DIFFRACTION1{ A|132-187 }A132 - 187
3X-RAY DIFFRACTION1{ A|269-296 }A296
4X-RAY DIFFRACTION2{ A|54-131 }A54 - 131
5X-RAY DIFFRACTION2{ A|188-268 }A188 - 268
6X-RAY DIFFRACTION3{ A|297-392 }A297 - 392
7X-RAY DIFFRACTION4{ B|1-53 }B1 - 53
8X-RAY DIFFRACTION4{ B|132-187 }B132 - 187
9X-RAY DIFFRACTION4{ B|269-296 }B269 - 296
10X-RAY DIFFRACTION5{ B|54-131 }B54 - 131
11X-RAY DIFFRACTION5{ B|188-268 }B188 - 268
12X-RAY DIFFRACTION6{ B|297-392 }B297 - 392

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