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- PDB-8sw7: BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody FP1 -

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Basic information

Entry
Database: PDB / ID: 8sw7
TitleBG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody FP1
Components
  • (BG505 Boost 2 ...) x 2
  • FP1 heavy chain
  • FP1 light chain
KeywordsVIRAL PROTEIN/Immune System / HIV-1 / Env / NHP / Antibody / Fusion Peptide / Polyclonal / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Biological speciesHuman immunodeficiency virus 1
Macaca mulatta (Rhesus monkey)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsPratap, P.P. / Antansijevic, A. / Ozorowski, G. / Ward, A.B.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136621 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI10066 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: bioRxiv / Year: 2023
Title: Focusing antibody responses to the fusion peptide in rhesus macaques.
Authors: Christopher A Cottrell / Payal P Pratap / Kimberly M Cirelli / Diane G Carnathan / Chiamaka A Enemuo / Aleksandar Antanasijevic / Gabriel Ozorowski / Leigh M Sewall / Hongmei Gao / Kelli M ...Authors: Christopher A Cottrell / Payal P Pratap / Kimberly M Cirelli / Diane G Carnathan / Chiamaka A Enemuo / Aleksandar Antanasijevic / Gabriel Ozorowski / Leigh M Sewall / Hongmei Gao / Kelli M Greene / Joel D Allen / Julia T Ngo / Yury Choe / Bartek Nogal / Murillo Silva / Jinal Bhiman / Matthias Pauthner / Darrell J Irvine / David Montefiori / Max Crispin / Dennis R Burton / Guido Silvestri / Shane Crotty / Andrew B Ward /
Abstract: Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies ...Immunodominance of antibodies targeting non-neutralizing epitopes and the high level of somatic hypermutation within germinal centers (GCs) required for most HIV broadly neutralizing antibodies (bnAbs) are major impediments to the development of an effective HIV vaccine. Rational protein vaccine design and non-conventional immunization strategies are potential avenues to overcome these hurdles. Here, we report using implantable osmotic pumps to continuously deliver a series of epitope-targeted immunogens to rhesus macaques over the course of six months to elicit immune responses against the conserved fusion peptide. Antibody specificities and GC responses were tracked longitudinally using electron microscopy polyclonal epitope mapping (EMPEM) and lymph node fine-needle aspirates, respectively. Application of cryoEMPEM delineated key residues for on-target and off-target responses that can drive the next round of structure-based vaccine design.
History
DepositionMay 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 6, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Data processing / Database references / Derived calculations / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / chem_comp_atom / chem_comp_bond / em_3d_reconstruction / em_admin / em_entity_assembly / entity / entity_poly / entity_poly_seq / entity_src_gen / entity_src_nat / pdbx_contact_author / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / software / struct_asym / struct_conf / struct_conn / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_3d_reconstruction.resolution / _em_admin.last_update ..._em_3d_reconstruction.resolution / _em_admin.last_update / _em_entity_assembly.entity_id_list / _entity.details / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_src_gen.entity_id / _entity_src_nat.entity_id / _entity_src_nat.pdbx_end_seq_num / _pdbx_database_status.pdb_format_compatible / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id / _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.ref_id / _struct_ref_seq.seq_align_end
Description: Model completeness
Details: Model completeness around N241 glycan region of the trimer near the FP1 epitope
Provider: author / Type: Coordinate replacement
Revision 2.1Nov 13, 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
H: FP1 heavy chain
L: FP1 light chain
A: BG505 Boost 2 gp120
B: BG505 Boost 2 gp41
C: BG505 Boost 2 gp120
D: BG505 Boost 2 gp41
E: BG505 Boost 2 gp41
F: BG505 Boost 2 gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,22760
Polymers245,6298
Non-polymers12,59952
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules HL

#1: Protein FP1 heavy chain


Mass: 10656.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The antibody sequence is not known as it is was directly isolated from macaque serum from blood draws in a polyclonal antibody sample.
Source: (natural) Macaca mulatta (Rhesus monkey)
#2: Protein FP1 light chain


Mass: 9124.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The antibody sequence is not known as it is was directly isolated from macaque serum from blood draws in a polyclonal antibody sample.
Source: (natural) Macaca mulatta (Rhesus monkey)

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BG505 Boost 2 ... , 2 types, 6 molecules ACFBDE

#3: Protein BG505 Boost 2 gp120


Mass: 58090.172 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#4: Protein BG505 Boost 2 gp41


Mass: 17192.574 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)

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Sugars , 2 types, 52 molecules

#5: 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
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 49 / 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
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: BG505 Boost 2 in complex with NHP Polyclonal Antibody FP1
Type: COMPLEX / Entity ID: #3-#4, #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.470 MDa / Experimental value: NO
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
150 mMTris1
2150 mMSodium Chloride1
30.005 mMLauryl Maltose Neopentyl Glycol1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 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 magnification: 22500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 41.3591843915 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7339

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63946 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02215389
ELECTRON MICROSCOPYf_angle_d1.70620926
ELECTRON MICROSCOPYf_dihedral_angle_d9.9515500
ELECTRON MICROSCOPYf_chiral_restr0.1272584
ELECTRON MICROSCOPYf_plane_restr0.0092613

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