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- EMDB-44893: Cryo-EM structure of rhesus antibody 41328-a.01 in complex with H... -

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Basic information

Entry
Database: EMDB / ID: EMD-44893
TitleCryo-EM structure of rhesus antibody 41328-a.01 in complex with HIV-1 Env BG505 DS-SOSIP
Map data
Sample
  • Complex: Complex of 41328-a.01 with HIV-1 BG505 envelope trimer
    • Protein or peptide: Envelope glycoprotein Gp120
    • Protein or peptide: Envelope glycoprotein Gp41
    • Protein or peptide: 41328-a.01 heavy chain
    • Protein or peptide: 41328-a.01 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeutralizing antibody / HIV-1 V2 apex / SHIV-elicited / Viral protein / IMMUNE SYSTEM / 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 / 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 / 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 speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsRoark RS / Shapiro L / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J Exp Med / Year: 2025
Title: Structural and genetic basis of HIV-1 envelope V2 apex recognition by rhesus broadly neutralizing antibodies.
Authors: Ryan S Roark / Rumi Habib / Jason Gorman / Hui Li / Andrew Jesse Connell / Mattia Bonsignori / Yicheng Guo / Michael P Hogarty / Adam S Olia / Kirsten J Sowers / Baoshan Zhang / Frederic ...Authors: Ryan S Roark / Rumi Habib / Jason Gorman / Hui Li / Andrew Jesse Connell / Mattia Bonsignori / Yicheng Guo / Michael P Hogarty / Adam S Olia / Kirsten J Sowers / Baoshan Zhang / Frederic Bibollet-Ruche / Tatsiana Bylund / Sean Callaghan / John W Carey / Gabriele Cerutti / Darcy R Harris / Wanting He / Emily Lewis / Tracy Liu / Rosemarie D Mason / Yujie Qiao / Younghoon Park / Juliette M Rando / Ajay Singh / Jeremy J Wolff / Q Paula Lei / Mark K Louder / Raiees Andrabi / Nicole A Doria-Rose / Kevin O Saunders / Michael S Seaman / Barton F Haynes / Daniel W Kulp / John R Mascola / Mario Roederer / Theodore C Pierson / Zizhang Sheng / Beatrice H Hahn / George M Shaw / Peter D Kwong / Lawrence Shapiro /
Abstract: Broadly neutralizing antibodies targeting the V2 apex of HIV-1 envelope are desired as vaccine design templates, but few have been described. Here, we report 11 lineages of V2 apex-neutralizing ...Broadly neutralizing antibodies targeting the V2 apex of HIV-1 envelope are desired as vaccine design templates, but few have been described. Here, we report 11 lineages of V2 apex-neutralizing antibodies from simian-human immunodeficiency virus (SHIV)-infected rhesus macaques and determine cryo-EM structures for 9. A single V2 apex-neutralizing lineage accounted for cross-clade breadth in most macaques, and somatic hypermutation relative to breadth was generally low, exemplified by antibody V033-a.01 with <5% nucleotide mutation and 37% breadth (208-strain panel). Envelope complex structures revealed eight different antibody classes (one multi-donor) and the complete repertoire of all five possible recognition topologies, recapitulating canonical human modes of apex insertion and C-strand hydrogen bonding. Despite this diversity in recognition, all rhesus-V2 apex antibodies were derived from reading frame two of the DH3-15*01 gene. Collectively, these results define-in rhesus-the structural and genetic basis of HIV-1 V2 apex recognition and demonstrate unprecedented structural plasticity of a highly selected immunogenetic element.
History
DepositionMay 15, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44893.png

Downloads & links

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Map

FileDownload / File: emd_44893.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.19460277 - 0.55810565
Average (Standard dev.)0.0011622616 (±0.01509098)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44893_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_44893_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of 41328-a.01 with HIV-1 BG505 envelope trimer

EntireName: Complex of 41328-a.01 with HIV-1 BG505 envelope trimer
Components
  • Complex: Complex of 41328-a.01 with HIV-1 BG505 envelope trimer
    • Protein or peptide: Envelope glycoprotein Gp120
    • Protein or peptide: Envelope glycoprotein Gp41
    • Protein or peptide: 41328-a.01 heavy chain
    • Protein or peptide: 41328-a.01 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of 41328-a.01 with HIV-1 BG505 envelope trimer

SupramoleculeName: Complex of 41328-a.01 with HIV-1 BG505 envelope trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: Envelope glycoprotein Gp120

MacromoleculeName: Envelope glycoprotein Gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.300348 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SACTQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ CMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG R

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Envelope glycoprotein Gp41

MacromoleculeName: Envelope glycoprotein Gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.075406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VGIGAVFLGF LGAAGSTMGA ASMTLTVQAR NLLSGIVQQQ SNLLRAPEAQ QHLLKLTVWG IKQLQARVLA VERYLRDQQL LGIWGCSGK LICCTNVPWN SSWSNRNLSE IWDNMTWLQW DKEISNYTQI IYGLLEESQN QQEKNEQDLL ALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: 41328-a.01 heavy chain

MacromoleculeName: 41328-a.01 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.56757 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQWGEG LVKPSETLSL SCAVYGGSIS GHYYWSWIRQ APGKGLEWIG KIDANSASTN YNPSFKNRVS ISKDTSKKQF YLNLHSVTA ADTAVYYCAR GSIYYEDDDG YYYSEATYLH LHLWGQGVVV TVSSASTKGP SVFPLAPSSR STSESTAALG C LVKDYFPE ...String:
QVQLQQWGEG LVKPSETLSL SCAVYGGSIS GHYYWSWIRQ APGKGLEWIG KIDANSASTN YNPSFKNRVS ISKDTSKKQF YLNLHSVTA ADTAVYYCAR GSIYYEDDDG YYYSEATYLH LHLWGQGVVV TVSSASTKGP SVFPLAPSSR STSESTAALG C LVKDYFPE PVTVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVEIKTCGG GL EVLFQ

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Macromolecule #4: 41328-a.01 light chain

MacromoleculeName: 41328-a.01 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 22.915264 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSA SEAARKRVSI SCSGSFSNIG TNSVSWYQHL PGTAPKLLIY HNGQRASGVS DRFSGSKSGT SASLAISALQ TEDEADYYC ATWDDMLNGY FFGAGTRLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVE VAWKADGSAV N AGVETTKP ...String:
QSVLTQPPSA SEAARKRVSI SCSGSFSNIG TNSVSWYQHL PGTAPKLLIY HNGQRASGVS DRFSGSKSGT SASLAISALQ TEDEADYYC ATWDDMLNGY FFGAGTRLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVE VAWKADGSAV N AGVETTKP SKQSNNKYAA SSYLSLTSDQ WKSHKSYSCQ VTHEGSTVEK TVAPAECS

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 24 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176070
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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