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- PDB-8rm1: Cryo-EM structure of a Foamy Virus fusion glycoprotein in the pos... -

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Basic information

Entry
Database: PDB / ID: 8rm1
TitleCryo-EM structure of a Foamy Virus fusion glycoprotein in the postfusion conformation
Components(Envelope glycoprotein gp130) x 2
KeywordsVIRUS / Envelope / Fusion / Spumavirus
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsFernandez, I. / Backovic, M.
Funding support France, 1items
OrganizationGrant numberCountry
Laboratories of Excellence (LabEx)ANR-LBX-62 IBEID France
CitationJournal: Sci Adv / Year: 2024
Title: Structures of the Foamy virus fusion protein reveal an unexpected link with the F protein of paramyxo- and pneumoviruses.
Authors: Ignacio Fernández / François Bontems / Delphine Brun / Youna Coquin / Casper A Goverde / Bruno E Correia / Antoine Gessain / Florence Buseyne / Felix A Rey / Marija Backovic /
Abstract: Foamy viruses (FVs) constitute a subfamily of retroviruses. Their envelope (Env) glycoprotein drives the merger of viral and cellular membranes during entry into cells. The only available structures ...Foamy viruses (FVs) constitute a subfamily of retroviruses. Their envelope (Env) glycoprotein drives the merger of viral and cellular membranes during entry into cells. The only available structures of retroviral Envs are those from human and simian immunodeficiency viruses from the subfamily of orthoretroviruses, which are only distantly related to the FVs. We report the cryo-electron microscopy structures of the FV Env ectodomain in the pre- and post-fusion states, which unexpectedly demonstrate structural similarity with the fusion protein (F) of paramyxo- and pneumoviruses, implying an evolutionary link between the viral fusogens. We describe the structural features that are unique to the FV Env and propose a mechanistic model for its conformational change, highlighting how the interplay of its structural elements could drive membrane fusion and viral entry. The structural knowledge on the FV Env now provides a framework for functional investigations, which can benefit the design of FV Env variants with improved features for use as gene therapy vectors.
History
DepositionJan 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 2.0Oct 30, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_branch_scheme / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _em_admin.last_update / _entity_src_gen.entity_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_src_id / _pdbx_branch_scheme.asym_id / _pdbx_branch_scheme.entity_id / _pdbx_branch_scheme.pdb_asym_id / _pdbx_entity_branch.entity_id / _pdbx_entity_branch_descriptor.entity_id / _pdbx_entity_branch_link.entity_id / _pdbx_entity_branch_list.entity_id / _pdbx_entity_nonpoly.entity_id / _pdbx_modification_feature.auth_asym_id / _pdbx_modification_feature.label_asym_id / _pdbx_modification_feature.label_seq_id / _pdbx_modification_feature.modified_residue_auth_asym_id / _pdbx_modification_feature.modified_residue_label_asym_id / _pdbx_modification_feature.modified_residue_label_seq_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Nov 20, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope glycoprotein gp130
D: Envelope glycoprotein gp130
B: Envelope glycoprotein gp130
E: Envelope glycoprotein gp130
C: Envelope glycoprotein gp130
F: Envelope glycoprotein gp130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,05315
Polymers282,3566
Non-polymers3,6969
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area62680 Å2
ΔGint-349 kcal/mol
Surface area107930 Å2
MethodPISA

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Components

#1: Protein Envelope glycoprotein gp130 / Env polyprotein


Mass: 52050.996 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian foamy virus / Gene: env / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: K7YEW5
#2: Protein Envelope glycoprotein gp130 / Env polyprotein


Mass: 42067.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian foamy virus / Gene: env / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: K7YEW5
#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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: 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
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Gorilla Foamy Virus Envelope glycoprotein / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Spumavirus
Source (recombinant)Organism: Drosophila melanogaster (fruit fly)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
11RELIONclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98407 / Num. of class averages: 2 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1

IDPDB-IDDetailsSource nameTypeAccession codeInitial refinement model-ID
1Phenix map to model tool followed by manual buildingOtherother
28AEZ

8aez

PDBexperimental model8AEZ2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318336
ELECTRON MICROSCOPYf_angle_d0.58224915
ELECTRON MICROSCOPYf_dihedral_angle_d4.292523
ELECTRON MICROSCOPYf_chiral_restr0.0432820
ELECTRON MICROSCOPYf_plane_restr0.0053153

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