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- EMDB-43879: Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R -

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Basic information

Entry
Database: EMDB / ID: EMD-43879
TitleCryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R
Map data
Sample
  • Complex: Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R
    • Protein or peptide: HIV-1 BG505 DS-SOSIP glycoprotein gp120
    • Protein or peptide: HIV-1 BG505 DS-SOSIP glycoprotein gp41
    • Protein or peptide: UCA3.G57R heavy chain
    • Protein or peptide: UCA3.G57R light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsEnvelope / Glycoprotein / Trimer / Antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 ...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 / identical protein binding / 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: 3.8 Å
AuthorsZhang QE / Acharya P
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI170752 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144371 United States
CitationJournal: Sci Transl Med / Year: 2025
Title: An engineered immunogen activates diverse HIV broadly neutralizing antibody precursors and promotes acquisition of improbable mutations.
Authors: Olivia M Swanson / Qianyi E Zhang / Elizabeth Van Itallie / Ming Tian / Alecia R Brown / Caitlin Harris / Anyway Brenda Kapingidza / Brianna Rhodes / Lena M Smith / Sravani Venkatayogi / ...Authors: Olivia M Swanson / Qianyi E Zhang / Elizabeth Van Itallie / Ming Tian / Alecia R Brown / Caitlin Harris / Anyway Brenda Kapingidza / Brianna Rhodes / Lena M Smith / Sravani Venkatayogi / Kenneth Cronin / McKenzie Frazier / Rob Parks / Maggie Bar / Chuancang Jiang / Joshua S Martin Beem / Hwei-Ling Cheng / Jillian Davis / Kelly McGovern / Amanda Newman / Robert J Edwards / Derek Cain / S Munir Alam / Kevin Wiehe / Kevin O Saunders / Priyamvada Acharya / Fred Alt / Barton F Haynes / Mihai L Azoitei /
Abstract: Elicitation of HIV broadly neutralizing antibodies (bnAbs) by vaccination first requires the activation of diverse precursors, followed by successive boosts that guide these responses to enhanced ...Elicitation of HIV broadly neutralizing antibodies (bnAbs) by vaccination first requires the activation of diverse precursors, followed by successive boosts that guide these responses to enhanced breadth through the acquisition of somatic mutations. Because HIV bnAbs contain mutations in their B cell receptors (BCRs) that are rarely generated during conventional B cell maturation, HIV vaccine immunogens must robustly engage and expand B cells with BCRs that contain these improbable mutations. Here, we engineered an immunogen that activates diverse precursors of an HIV V3-glycan bnAb and promotes their acquisition of a functionally critical improbable mutation. This immunogen was validated biochemically, structurally, and in three different humanized immunoglobulin mouse models that were designed to test HIV immunogens. These results provide a blueprint for rationally designing priming immunogens that explicitly target the elicitation of antibodies with functional yet improbable mutations.
History
DepositionFeb 29, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43879.png

Downloads & links

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Map

FileDownload / File: emd_43879.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: 0.2
Minimum - Maximum-0.9961061 - 1.2321146
Average (Standard dev.)0.00066970504 (±0.029167602)
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_43879_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_43879_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 : Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R

EntireName: Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R
Components
  • Complex: Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R
    • Protein or peptide: HIV-1 BG505 DS-SOSIP glycoprotein gp120
    • Protein or peptide: HIV-1 BG505 DS-SOSIP glycoprotein gp41
    • Protein or peptide: UCA3.G57R heavy chain
    • Protein or peptide: UCA3.G57R light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R

SupramoleculeName: Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 BG505 DS-SOSIP glycoprotein gp120

MacromoleculeName: HIV-1 BG505 DS-SOSIP glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Details: d949.GS-gp120 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.505453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ICSDAGSGGV EEMKNCSFNT TTEIRDKEKK EYALFYKPDI VPLSETNNTS EYRLINCNTS A CTQACPKV ...String:
AENLWVTVYY GVPVWKEAKT TLFCASDARA YEKEVHNVWA THACVPTDPS PQELVLGNVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ICSDAGSGGV EEMKNCSFNT TTEIRDKEKK EYALFYKPDI VPLSETNNTS EYRLINCNTS A CTQACPKV TFEPIPIHYC APAGYAILKC NDETFNGTGP CSNVSTVQCT HGIRPVVSTQ LLLNGSLAEK EIVIRSENLT NN AKIIIVH LHTPVEIVCT RPNNNTRKSV RIGPGQTFYA TGDIIGDIKQ AHCNISEEKW NDTLQKVGIE LQKHFPNKTI KYN QSAGGD MEITTHSFNC GGEFFYCNTS NLFNGTYNGT YISTNSSANS TSTITLQCRI KQIINMWQGV GRCMYAPPIA GNIT CRSNI TGLLLTRDGG TNSNETETFR PAGGDMRDNW RSELYKYKVV KIEPLGVAPT RCKRRVVGRR RRRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: HIV-1 BG505 DS-SOSIP glycoprotein gp41

MacromoleculeName: HIV-1 BG505 DS-SOSIP glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Details: d949.GS-gp41 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: UCA3.G57R heavy chain

MacromoleculeName: UCA3.G57R heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.081082 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYTFT GYYMHWVRQA PGQGLEWMGW INPNSGRTNY AQKFQGRVTM TRDTSISTAY MELSRLRSD DTAVYYCARG GWISLYYDSS GYPNFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT GYYMHWVRQA PGQGLEWMGW INPNSGRTNY AQKFQGRVTM TRDTSISTAY MELSRLRSD DTAVYYCARG GWISLYYDSS GYPNFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKRVEPK SCDK

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Macromolecule #4: UCA3.G57R light chain

MacromoleculeName: UCA3.G57R light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.719115 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPASV SGSPGQSITI SCTGTSSDVG SYNLVSWYQQ HPGKAPKLMI YEVSKRPSGV SNRFSGSKSG NTASLTISGL QAEDEADYY CCSYAGSSTV IFGGGTKLTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSALTQPASV SGSPGQSITI SCTGTSSDVG SYNLVSWYQQ HPGKAPKLMI YEVSKRPSGV SNRFSGSKSG NTASLTISGL QAEDEADYY CCSYAGSSTV IFGGGTKLTV LGQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 27 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration1.2 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 8083 / Average electron dose: 66.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.35000000000000003 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3521284
Startup modelType of model: NONE / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 362409
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9aug:
Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R

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