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- EMDB-43232: CH235.12 Fab bound to the HIV-1 CH505.M5 SOSIP -

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Basic information

Entry
Database: EMDB / ID: EMD-43232
TitleCH235.12 Fab bound to the HIV-1 CH505.M5 SOSIP
Map data
Sample
  • Complex: Antibody Fab bound HIV-1 ectodomain
    • Protein or peptide: CH505.M5.G458Y SOSIP gp120
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: CH235.12 Fab Heavy Chain
    • Protein or peptide: CH235.12 Fab Light Chain
KeywordsImmunogen / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.31 Å
AuthorsHenderson R / Acharya P
Funding support United States, 4 items
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, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43232.png

Downloads & links

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Map

FileDownload / File: emd_43232.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-5.5988135 - 6.97258
Average (Standard dev.)0.0034482984 (±0.12440251)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43232_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43232_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Antibody Fab bound HIV-1 ectodomain

EntireName: Antibody Fab bound HIV-1 ectodomain
Components
  • Complex: Antibody Fab bound HIV-1 ectodomain
    • Protein or peptide: CH505.M5.G458Y SOSIP gp120
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: CH235.12 Fab Heavy Chain
    • Protein or peptide: CH235.12 Fab Light Chain

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Supramolecule #1: Antibody Fab bound HIV-1 ectodomain

SupramoleculeName: Antibody Fab bound HIV-1 ectodomain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: CH505.M5.G458Y SOSIP gp120

MacromoleculeName: CH505.M5.G458Y SOSIP gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.246586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKKVHNVWA THACVPTDPN PQEMVLKNVT ENFNMWKNDM VDQMHEDVIS LWDQSLKPC VKLTPLCVTL NCTNATASNS SIIEGMKNCS FNITTELRDK REKKNALFYK LDIVQLDGNS SQYRLINCNT S VITQACPK ...String:
AENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKKVHNVWA THACVPTDPN PQEMVLKNVT ENFNMWKNDM VDQMHEDVIS LWDQSLKPC VKLTPLCVTL NCTNATASNS SIIEGMKNCS FNITTELRDK REKKNALFYK LDIVQLDGNS SQYRLINCNT S VITQACPK VSFDPIPIHY CAPAGYAILK CNNKTFTGTG PCNNVSTVQC THGIKPVVST QLLLNGSLAE GEIIIRSENI TK NVKTIIV HLNESVKIEC TRPNNKTRTS IRIGPGQWFY ATGQVIGDIR EAYCNINESK WNETLQRVSK KLKEYFPHKN ITF QPSSGG DLEITTHSFN CGGEFFYCNT SSLFNRTYMA NSTDMANSTE TNSTRTITIH CRIKQIINMW QEVGRAMYAP PIAG NITCI SNITGLLLTR DYGKNNTETF RPGGGNMKDN WRSELYKYKV VKIEPLGVAP TRCKRRVVG

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 18.089646 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RRRRRRAVGI GAVFLGFLGA AGSTMGAASM TLTVQARNLL SGIVQQQSNL LRAPEAQQHL LKLTVWGIKQ LQARVLAVER YLRDQQLLG IWGCSGKLIC CTNVPWNSSW SNRNLSEIWD NMTWLQWDKE ISNYTQIIYG LLEESQNQQE KNEQDLLALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: CH235.12 Fab Heavy Chain

MacromoleculeName: CH235.12 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.319373 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVRLAQYGGG VKRLGATMTL SCVASGYTFN DYYIHWVRQA PGQGFELLGY IDPANGRPDY AGALRERLSF YRDKSMETLY MDLRSLRYD DTAMYYCVRN VGTAGSLLHY DHWGSGSPVI VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVRLAQYGGG VKRLGATMTL SCVASGYTFN DYYIHWVRQA PGQGFELLGY IDPANGRPDY AGALRERLSF YRDKSMETLY MDLRSLRYD DTAMYYCVRN VGTAGSLLHY DHWGSGSPVI VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSC

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Macromolecule #4: CH235.12 Fab Light Chain

MacromoleculeName: CH235.12 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.450996 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT LSASPGERVT LTCRASRSVR NNVAWYQHKG GQSPRLLIYD ASTRAAGVPA RFSGSASGTE FTLAISNLES EDFTVYFCL QYNNWWTFGQ GTRVDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
EIVLTQSPAT LSASPGERVT LTCRASRSVR NNVAWYQHKG GQSPRLLIYD ASTRAAGVPA RFSGSASGTE FTLAISNLES EDFTVYFCL QYNNWWTFGQ GTRVDIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.1
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 148858
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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