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- PDB-8aez: X-ray structure of the deglycosylated receptor binding domain of ... -

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Basic information

Entry
Database: PDB / ID: 8aez
TitleX-ray structure of the deglycosylated receptor binding domain of Env glycoprotein of Simian Foamy virus
ComponentsEnvelope glycoprotein gp130
KeywordsVIRAL PROTEIN / Receptor binding domain
Function / homologyFoamy virus envelope protein / Foamy virus envelope protein / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane / Envelope glycoprotein gp130
Function and homology information
Biological speciesSimian foamy virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.574 Å
AuthorsBackovic, M.
Funding support France, 1items
OrganizationGrant numberCountry
Laboratories of Excellence (LabEx) France
CitationJournal: Nat Commun / Year: 2023
Title: The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells.
Authors: Fernandez, I. / Dynesen, L.T. / Coquin, Y. / Pederzoli, R. / Brun, D. / Haouz, A. / Gessain, A. / Rey, F.A. / Buseyne, F. / Backovic, M.
History
DepositionJul 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein gp130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3788
Polymers40,2891
Non-polymers3,0907
Water55831
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)99.451, 99.451, 120.609
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Envelope glycoprotein gp130 / Env polyprotein


Mass: 40288.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian foamy virus / Gene: env / Variant: BAK74 / Cell line (production host): 2 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider / References: UniProt: K7YEW5
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: 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.: 5 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.97 Å3/Da / Density % sol: 69.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 3.5M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.574→49.73 Å / Num. obs: 22363 / % possible obs: 99.91 % / Redundancy: 20.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.2051 / Rpim(I) all: 0.04701 / Net I/σ(I): 10.1
Reflection shellResolution: 2.574→2.666 Å / Rmerge(I) obs: 0.9362 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 2101 / CC1/2: 0.846 / Rpim(I) all: 0.2117

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDS`data reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.574→49.73 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.289 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.285 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.236
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1052 -RANDOM
Rwork0.2134 ---
obs0.2153 22357 99.9 %-
Displacement parametersBiso mean: 75.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.6373 Å20 Å20 Å2
2--1.6373 Å20 Å2
3----3.2747 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.574→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2711 0 203 31 2945
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083016HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.984129HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1069SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes490HARMONIC5
X-RAY DIFFRACTIONt_it3016HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion426SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2143SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion16.74
LS refinement shellResolution: 2.574→49.73 Å
RfactorNum. reflection% reflection
Rfree0.2989 22 -
Rwork0.2885 --
obs--98.06 %
Refinement TLS params.Origin x: -22.1361 Å / Origin y: -36.3317 Å / Origin z: 18.3941 Å
111213212223313233
T-0.0924 Å2-0.0031 Å20.0474 Å2-0.0644 Å2-0.0598 Å2---0.0778 Å2
L3.0074 °2-1.3078 °21.099 °2-0.8424 °2-0.7704 °2--1.9227 °2
S0.0412 Å °0.055 Å °-0.11 Å °0.055 Å °0.0847 Å °-0.1245 Å °-0.11 Å °-0.1245 Å °-0.1259 Å °
Refinement TLS groupSelection details: { A|* }

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