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- PDB-8d0y: Crystal Structure of HIV-1 BG505 SOSIPv8 Trimer in Complex with C... -

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Basic information

Entry
Database: PDB / ID: 8d0y
TitleCrystal Structure of HIV-1 BG505 SOSIPv8 Trimer in Complex with CD4bs targeting antibody 21N13 and interface targeting antibody 35O22 at 4.7 Angstrom
Components
  • (BG505SOSIPv8 ...) x 2
  • 21N13 Fab Heavy Chain
  • 21N13 Fab Light Chain
  • 35O22scFv Heavy Chain Variable
  • 35O22scFv Light Chain Variable
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 CD4bs antibody / HIV-1 Envelop Protein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.7 Å
AuthorsXian, Y. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
International AIDS Vaccine InitiativeINV-008352/OPP1153692 United States
Consortia for HIV/AIDS Vaccine DevelopmentCHAVD 1UM1 AI144462 United States
Other privateP01 AI110657
CitationJournal: Sci Immunol / Year: 2024
Title: Germline-targeting HIV vaccination induces neutralizing antibodies to the CD4 binding site.
Authors: Tom G Caniels / Max Medina-Ramìrez / Shiyu Zhang / Sven Kratochvil / Yuejiao Xian / Ja-Hyun Koo / Ronald Derking / Jakob Samsel / Jelle van Schooten / Simone Pecetta / Edward Lamperti / ...Authors: Tom G Caniels / Max Medina-Ramìrez / Shiyu Zhang / Sven Kratochvil / Yuejiao Xian / Ja-Hyun Koo / Ronald Derking / Jakob Samsel / Jelle van Schooten / Simone Pecetta / Edward Lamperti / Meng Yuan / María Ríos Carrasco / Iván Del Moral Sánchez / Joel D Allen / Joey H Bouhuijs / Anila Yasmeen / Thomas J Ketas / Jonne L Snitselaar / Tom P L Bijl / Isabel Cuella Martin / Jonathan L Torres / Albert Cupo / Lisa Shirreff / Kenneth Rogers / Rosemarie D Mason / Mario Roederer / Kelli M Greene / Hongmei Gao / Catarina Mendes Silva / Isabel J L Baken / Ming Tian / Frederick W Alt / Bali Pulendran / Michael S Seaman / Max Crispin / Marit J van Gils / David C Montefiori / Adrian B McDermott / François J Villinger / Richard A Koup / John P Moore / Per Johan Klasse / Gabriel Ozorowski / Facundo D Batista / Ian A Wilson / Andrew B Ward / Rogier W Sanders /
Abstract: Eliciting potent and broadly neutralizing antibodies (bnAbs) is a major goal in HIV-1 vaccine development. Here, we describe how germline-targeting immunogen BG505 SOSIP germline trimer 1.1 (GT1.1), ...Eliciting potent and broadly neutralizing antibodies (bnAbs) is a major goal in HIV-1 vaccine development. Here, we describe how germline-targeting immunogen BG505 SOSIP germline trimer 1.1 (GT1.1), generated through structure-based design, engages a diverse range of VRC01-class bnAb precursors. A single immunization with GT1.1 expands CD4 binding site (CD4bs)-specific VRC01-class B cells in knock-in mice and drives VRC01-class maturation. In nonhuman primates (NHPs), GT1.1 primes CD4bs-specific neutralizing serum responses. Selected monoclonal antibodies (mAbs) isolated from GT1.1-immunized NHPs neutralize fully glycosylated BG505 virus. Two mAbs, 12C11 and 21N13, neutralize subsets of diverse heterologous neutralization-resistant viruses. High-resolution structures revealed that 21N13 targets the same conserved residues in the CD4bs as VRC01-class and CH235-class bnAbs despite its low sequence similarity (~40%), whereas mAb 12C11 binds predominantly through its heavy chain complementarity-determining region 3. These preclinical data underpin the ongoing evaluation of GT1.1 in a phase 1 clinical trial in healthy volunteers.
History
DepositionMay 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Nov 22, 2023Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3May 15, 2024Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.5Jan 14, 2026Group: Database references / Structure summary / Category: citation / citation_author / entity
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 / _entity.details / _entity.pdbx_description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 35O22scFv Heavy Chain Variable
E: 35O22scFv Light Chain Variable
H: 21N13 Fab Heavy Chain
L: 21N13 Fab Light Chain
G: BG505SOSIPv8 gp120
B: BG505SOSIPv8 gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,90722
Polymers141,7956
Non-polymers10,11116
Water00
1
D: 35O22scFv Heavy Chain Variable
E: 35O22scFv Light Chain Variable
H: 21N13 Fab Heavy Chain
L: 21N13 Fab Light Chain
G: BG505SOSIPv8 gp120
B: BG505SOSIPv8 gp41
hetero molecules

D: 35O22scFv Heavy Chain Variable
E: 35O22scFv Light Chain Variable
H: 21N13 Fab Heavy Chain
L: 21N13 Fab Light Chain
G: BG505SOSIPv8 gp120
B: BG505SOSIPv8 gp41
hetero molecules

D: 35O22scFv Heavy Chain Variable
E: 35O22scFv Light Chain Variable
H: 21N13 Fab Heavy Chain
L: 21N13 Fab Light Chain
G: BG505SOSIPv8 gp120
B: BG505SOSIPv8 gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,72066
Polymers425,38618
Non-polymers30,33448
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)264.672, 264.672, 264.672
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3

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Components

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Protein , 1 types, 1 molecules D

#1: Protein 35O22scFv Heavy Chain Variable


Mass: 14130.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

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BG505SOSIPv8 ... , 2 types, 2 molecules GB

#5: Protein BG505SOSIPv8 gp120


Mass: 51243.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#6: Protein BG505SOSIPv8 gp41


Mass: 16616.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)

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Antibody , 3 types, 3 molecules EHL

#2: Antibody 35O22scFv Light Chain Variable


Mass: 12056.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Antibody 21N13 Fab Heavy Chain


Mass: 24334.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#4: Antibody 21N13 Fab Light Chain


Mass: 23413.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

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Sugars , 7 types, 16 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 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.: 2
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
#9: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-2)-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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#11: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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: 910.823 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#12: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#13: 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.: 6
Source method: isolated from a genetically manipulated source
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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 10.9 Å3/Da / Density % sol: 88.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium acetate, pH5.5,1.75M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4.7→43.63 Å / Num. obs: 32440 / % possible obs: 98.9 % / Redundancy: 20.4 % / Biso Wilson estimate: 276 Å2 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.05 / Rrim(I) all: 0.24 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) all% possible allRrim(I) all
4.7-4.782.72.916640.051.866.2
4.96-5.0610.72.8816240.2570.9071003.031

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cez

5cez


Resolution: 4.7→43.63 Å / SU ML: 0.9495 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2978 1573 4.99 %
Rwork0.2683 29954 -
obs0.2698 31527 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 351.65 Å2
Refinement stepCycle: LAST / Resolution: 4.7→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9950 0 672 0 10622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004110853
X-RAY DIFFRACTIONf_angle_d0.875514762
X-RAY DIFFRACTIONf_chiral_restr0.0521812
X-RAY DIFFRACTIONf_plane_restr0.00441798
X-RAY DIFFRACTIONf_dihedral_angle_d12.99194103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.7-4.830.3725860.39711718X-RAY DIFFRACTION61.28
4.83-5.010.37191360.36092771X-RAY DIFFRACTION98.71
5.01-5.210.38821490.3552808X-RAY DIFFRACTION99.97
5.21-5.440.36321630.33332784X-RAY DIFFRACTION100
5.44-5.730.36261230.31922814X-RAY DIFFRACTION100
5.73-6.090.35381390.32992812X-RAY DIFFRACTION100
6.09-6.560.39051530.31842846X-RAY DIFFRACTION99.97
6.56-7.210.34661730.33192796X-RAY DIFFRACTION100
7.22-8.250.31731300.26312845X-RAY DIFFRACTION100
8.26-10.380.24051540.21272864X-RAY DIFFRACTION100
10.39-43.630.26291670.23572896X-RAY DIFFRACTION98.74

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