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- EMDB-43233: CH505.M5.G458Y CE2 Design SOSIP -

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Basic information

Entry
Database: EMDB / ID: EMD-43233
TitleCH505.M5.G458Y CE2 Design SOSIP
Map data
Sample
  • Complex: HIV-1 ectodomain
    • Protein or peptide: CH505.CE2 SOSIP gp120
    • Protein or peptide: CH505.CE2 SOSIP gp41
KeywordsImmunogen / Vaccine / Antibody / VIRAL PROTEIN
Function / homology
Function and homology information


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 ...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
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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_43233.png

Downloads & links

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Map

FileDownload / File: emd_43233.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 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: 2.88
Minimum - Maximum-11.677167000000001 - 17.187462
Average (Standard dev.)0.0045058345 (±0.29962376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43233_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43233_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 : HIV-1 ectodomain

EntireName: HIV-1 ectodomain
Components
  • Complex: HIV-1 ectodomain
    • Protein or peptide: CH505.CE2 SOSIP gp120
    • Protein or peptide: CH505.CE2 SOSIP gp41

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Supramolecule #1: HIV-1 ectodomain

SupramoleculeName: 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.CE2 SOSIP gp120

MacromoleculeName: CH505.CE2 SOSIP gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 51.373711 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNVWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS V ITQACPKV ...String:
ENLWVTVYYG VPVWKEAKTT LFCASDAKAY EKEVHNVWAT HACVPTDPNP QEMVLKNVTE NFNMWKNDMV DQMHEDVISL WDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS V ITQACPKV SFDPIPIHYC APAGYAILKC NNKTFTGTGP CNNVSTVQCT HGIKPVVSTQ LLLNGSLAEG EIIIRSENIT KN VKTIIVH LNESVKIECT RPNNKTRTSI RIGPGQAFYA TGQVIGDIRE AYCNINESKW NETLQRVSKK LKEYFPHKNI TFQ PSSGGD LEITTHSFNC GGEFFYCNTS SLFNRTYMAN STETNSTRTI TIHCRIKQII NMWQEVGRAM YAPPIAGNIT CISN ITGLL LTRCYGKNNT ECFRPGGGNM KDNWRSELYK YKVVKIEPLG VAPTRCKRRV V

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: CH505.CE2 SOSIP gp41

MacromoleculeName: CH505.CE2 SOSIP gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 16.683998 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VFLGFLGAAG STMGAASMTL TVQARNLLSG IVQQQSNLLK AIEAQQHMLK LTVWGIKQLQ ARVLAVERYL RDQQLLGIWG CSGKLICCT NVPWNSSWSN RNLSEIWDNM TWLQWDKEIS NYTQIIYGLL EESQNQQEKN EQDLLALD

UniProtKB: Envelope glycoprotein gp160

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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: 60.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.62 µm / Nominal defocus min: 0.46 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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106813
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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