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- PDB-7ryu: Anti-HIV neutralizing antibody Ab1303 Fab isolated from sequentia... -

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Basic information

Entry
Database: PDB / ID: 7ryu
TitleAnti-HIV neutralizing antibody Ab1303 Fab isolated from sequentially immunized mcaques
Components
  • Ab1303 Fab heavy chain
  • Ab1303 Fab light chain
KeywordsIMMUNE SYSTEM / anti-HIV neutralizing antibody / antibody Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsYang, Z. / Bjorkman, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HIVRAD P01 AI100148 United States
Bill & Melinda Gates FoundationCAVD INV-002143 United States
CitationJournal: Nat Commun / Year: 2022
Title: Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer.
Authors: Zhi Yang / Kim-Marie A Dam / Michael D Bridges / Magnus A G Hoffmann / Andrew T DeLaitsch / Harry B Gristick / Amelia Escolano / Rajeev Gautam / Malcolm A Martin / Michel C Nussenzweig / ...Authors: Zhi Yang / Kim-Marie A Dam / Michael D Bridges / Magnus A G Hoffmann / Andrew T DeLaitsch / Harry B Gristick / Amelia Escolano / Rajeev Gautam / Malcolm A Martin / Michel C Nussenzweig / Wayne L Hubbell / Pamela J Bjorkman /
Abstract: Broadly-neutralizing antibodies (bNAbs) against HIV-1 Env can protect from infection. We characterize Ab1303 and Ab1573, heterologously-neutralizing CD4-binding site (CD4bs) antibodies, isolated from ...Broadly-neutralizing antibodies (bNAbs) against HIV-1 Env can protect from infection. We characterize Ab1303 and Ab1573, heterologously-neutralizing CD4-binding site (CD4bs) antibodies, isolated from sequentially-immunized macaques. Ab1303/Ab1573 binding is observed only when Env trimers are not constrained in the closed, prefusion conformation. Fab-Env cryo-EM structures show that both antibodies recognize the CD4bs on Env trimer with an 'occluded-open' conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4. The occluded-open Env trimer conformation includes outwardly-rotated gp120 subunits, but unlike CD4-bound Envs, does not exhibit V1V2 displacement, 4-stranded gp120 bridging sheet, or co-receptor binding site exposure. Inter-protomer distances within trimers measured by double electron-electron resonance spectroscopy suggest an equilibrium between occluded-open and closed Env conformations, consistent with Ab1303/Ab1573 binding stabilizing an existing conformation. Studies of Ab1303/Ab1573 demonstrate that CD4bs neutralizing antibodies that bind open Env trimers can be raised by immunization, thereby informing immunogen design and antibody therapeutic efforts.
History
DepositionAug 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: 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.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Ab1303 Fab heavy chain
L: Ab1303 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,7582
Polymers48,7582
Non-polymers00
Water12,250680
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-22 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.853, 66.973, 136.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Ab1303 Fab heavy chain


Mass: 25338.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody Ab1303 Fab light chain


Mass: 23419.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 293.15 K / Method: evaporation
Details: 10% (v/v) PEG 200, 0.1M Bis-Tris propane (pH 9.0), and 18% w/v PEG 8,000

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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 EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.51→38.3 Å / Num. obs: 177690 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 20.66 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.5
Reflection shellResolution: 1.51→1.53 Å / Redundancy: 11.4 % / Num. unique obs: 9145 / CC1/2: 0.8 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
TRUNCATEdata reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YK4

4yk4


Resolution: 1.51→38.27 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 3865 2.18 %
Rwork0.1803 173825 -
obs0.1807 177690 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.6 Å2 / Biso mean: 27.0334 Å2 / Biso min: 12.11 Å2
Refinement stepCycle: final / Resolution: 1.51→38.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 0 680 4010
Biso mean---39.24 -
Num. residues----440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.51-1.530.31391410.2866086622797
1.53-1.550.28331330.262161526285100
1.55-1.570.27091460.255362796425100
1.57-1.590.28731310.250262056336100
1.59-1.610.25131420.246661656307100
1.61-1.640.25391280.245662626390100
1.64-1.660.31071310.258661436274100
1.66-1.690.27041710.247662296400100
1.69-1.720.28741150.234262786393100
1.72-1.750.25421570.227961586315100
1.75-1.780.25291270.21762276354100
1.78-1.820.2411360.213662266362100
1.82-1.860.20871430.208761836326100
1.86-1.90.2541250.203562326357100
1.9-1.950.19451700.210562026372100
1.95-20.25361290.20262006329100
2-2.060.18691340.200262656399100
2.06-2.130.21391480.184261606308100
2.13-2.20.21371190.186162766395100
2.2-2.290.23941460.180561756321100
2.29-2.40.20461410.187562316372100
2.4-2.520.18151180.180661876305100
2.52-2.680.21311420.189462376379100
2.68-2.890.19111390.177962336372100
2.89-3.180.21380.169362266364100
3.18-3.640.16021320.156461636295100
3.64-4.580.15341440.139162536397100
4.58-38.270.1641390.148361926331100

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