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- PDB-8aic: X-ray structure of the receptor binding domain of Env glycoprotei... -

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Basic information

Entry
Database: PDB / ID: 8aic
TitleX-ray structure of the 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBackovic, M. / Fernandez, I.
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 26, 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 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein gp130
B: Envelope glycoprotein gp130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,56515
Polymers80,5772
Non-polymers7,98813
Water1,928107
1
A: Envelope glycoprotein gp130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4157
Polymers40,2891
Non-polymers4,1276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Envelope glycoprotein gp130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1508
Polymers40,2891
Non-polymers3,8627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.624, 123.624, 191.611
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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Protein / Non-polymers , 2 types, 109 molecules AB

#1: Protein Envelope glycoprotein gp130 / Env polyprotein


Mass: 40288.566 Da / Num. of mol.: 2
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): Scneider / References: UniProt: K7YEW5
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 13 molecules

#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.: 4
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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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-(1-2)-alpha-D-mannopyranose-(1-6)-[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: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 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]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: 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)]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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 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]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: 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 / N-Acetylglucosamine


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

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Details

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: 5.25 Å3/Da / Density % sol: 76.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium tartarate, 20% w/v PEG 3350

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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: 2.8→46.73 Å / Num. obs: 40619 / % possible obs: 99.58 % / Redundancy: 21.6 % / Biso Wilson estimate: 70.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.04364 / Net I/σ(I): 13.35
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 21.6 % / Rmerge(I) obs: 1.705 / Num. unique obs: 4041 / CC1/2: 0.689 / Rpim(I) all: 0.3719 / % possible all: 99.14

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Related deposition D_1292124233

Resolution: 2.8→46.73 Å / SU ML: 0.4391 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9352
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 2113 5.2 %
Rwork0.1942 38547 -
obs0.1961 40615 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.54 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5432 0 547 107 6086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00436139
X-RAY DIFFRACTIONf_angle_d0.76098345
X-RAY DIFFRACTIONf_chiral_restr0.0492996
X-RAY DIFFRACTIONf_plane_restr0.00611007
X-RAY DIFFRACTIONf_dihedral_angle_d9.9891076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.860.43681380.42572548X-RAY DIFFRACTION98.28
2.86-2.940.43871440.35712564X-RAY DIFFRACTION99.45
2.94-3.010.35221350.2882580X-RAY DIFFRACTION99.45
3.01-3.10.30161420.24412527X-RAY DIFFRACTION99.33
3.1-3.20.3053940.23492607X-RAY DIFFRACTION99.52
3.2-3.320.27081320.22942541X-RAY DIFFRACTION99.55
3.32-3.450.28361380.24732604X-RAY DIFFRACTION99.64
3.45-3.610.28041350.24662558X-RAY DIFFRACTION99.63
3.61-3.80.20951480.17042544X-RAY DIFFRACTION99.63
3.8-4.040.20731500.15922588X-RAY DIFFRACTION99.71
4.04-4.350.20261350.14642582X-RAY DIFFRACTION99.89
4.35-4.780.16481290.14712583X-RAY DIFFRACTION99.82
4.78-5.480.20281580.15212559X-RAY DIFFRACTION99.85
5.48-6.890.21041530.19112601X-RAY DIFFRACTION99.96
6.9-46.730.20161820.18432561X-RAY DIFFRACTION99.6
Refinement TLS params.Method: refined / Origin x: 37.3339561032 Å / Origin y: 43.2539780996 Å / Origin z: 29.6017111713 Å
111213212223313233
T0.306734165676 Å2-0.000928783116923 Å20.0370025467479 Å2-0.3585857523 Å20.0617885159651 Å2--0.418169753988 Å2
L1.13631787441 °2-0.348750620115 °20.815021785019 °2-0.462938307611 °2-0.400236378297 °2--1.68076303091 °2
S0.00245712235467 Å °-0.269543320402 Å °-0.159184213251 Å °0.0463820026903 Å °0.119337242762 Å °0.150445826828 Å °-0.0648325225016 Å °-0.235327497186 Å °-0.120010809704 Å °
Refinement TLS groupSelection details: all

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