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- PDB-8vh2: CH235.12 Fab bound to the HIV-1 CH505.M5 SOSIP -

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Basic information

Entry
Database: PDB / ID: 8vh2
TitleCH235.12 Fab bound to the HIV-1 CH505.M5 SOSIP
Components
  • CH235.12 Fab Heavy Chain
  • CH235.12 Fab Light Chain
  • CH505.M5.G458Y SOSIP gp120
  • Envelope glycoprotein gp160
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Immunogen / Vaccine / Antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated perturbation of host defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.31 Å
AuthorsHenderson, R. / Acharya, P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP2-AI164323 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1AI144371 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI145687 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170752 United States
CitationJournal: Nat Commun / Year: 2024
Title: Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies.
Authors: Rory Henderson / Kara Anasti / Kartik Manne / Victoria Stalls / Carrie Saunders / Yishak Bililign / Ashliegh Williams / Pimthada Bubphamala / Maya Montani / Sangita Kachhap / Jingjing Li / ...Authors: Rory Henderson / Kara Anasti / Kartik Manne / Victoria Stalls / Carrie Saunders / Yishak Bililign / Ashliegh Williams / Pimthada Bubphamala / Maya Montani / Sangita Kachhap / Jingjing Li / Chuancang Jaing / Amanda Newman / Derek W Cain / Xiaozhi Lu / Sravani Venkatayogi / Madison Berry / Kshitij Wagh / Bette Korber / Kevin O Saunders / Ming Tian / Fred Alt / Kevin Wiehe / Priyamvada Acharya / S Munir Alam / Barton F Haynes /
Abstract: Vaccine development targeting rapidly evolving pathogens such as HIV-1 requires induction of broadly neutralizing antibodies (bnAbs) with conserved paratopes and mutations, and in some cases, the ...Vaccine development targeting rapidly evolving pathogens such as HIV-1 requires induction of broadly neutralizing antibodies (bnAbs) with conserved paratopes and mutations, and in some cases, the same Ig-heavy chains. The current trial-and-error search for immunogen modifications that improve selection for specific bnAb mutations is imprecise. Here, to precisely engineer bnAb boosting immunogens, we use molecular dynamics simulations to examine encounter states that form when antibodies collide with the HIV-1 Envelope (Env). By mapping how bnAbs use encounter states to find their bound states, we identify Env mutations predicted to select for specific antibody mutations in two HIV-1 bnAb B cell lineages. The Env mutations encode antibody affinity gains and select for desired antibody mutations in vivo. These results demonstrate proof-of-concept that Env immunogens can be designed to directly select for specific antibody mutations at residue-level precision by vaccination, thus demonstrating the feasibility of sequential bnAb-inducing HIV-1 vaccine design.
History
DepositionDec 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CH505.M5.G458Y SOSIP gp120
B: Envelope glycoprotein gp160
C: CH235.12 Fab Heavy Chain
D: CH235.12 Fab Light Chain
E: CH505.M5.G458Y SOSIP gp120
F: Envelope glycoprotein gp160
G: CH235.12 Fab Heavy Chain
H: CH235.12 Fab Light Chain
I: CH505.M5.G458Y SOSIP gp120
J: Envelope glycoprotein gp160
K: CH235.12 Fab Heavy Chain
L: CH235.12 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)354,32012
Polymers354,32012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CH505.M5.G458Y SOSIP gp120 / Env polyprotein


Mass: 52246.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: M4M5H1
#2: Protein Envelope glycoprotein gp160 / Env polyprotein


Mass: 18089.646 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: M4M5H1
#3: Antibody CH235.12 Fab Heavy Chain


Mass: 24319.373 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody CH235.12 Fab Light Chain


Mass: 23450.996 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: Antibody Fab bound HIV-1 ectodomain / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Homo sapiens (human)
Details of virusIsolate: OTHER / Type: VIRION
Buffer solutionpH: 7.1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 3400 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 59.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148858 / Symmetry type: POINT

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