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- EMDB-46914: Q23.MD39 in Complex with Fab from antibody 35O22 -

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Basic information

Entry
Database: EMDB / ID: EMD-46914
TitleQ23.MD39 in Complex with Fab from antibody 35O22
Map data
Sample
  • Complex: Q23.MD39 Env trimer in Complex with 35O22
    • Complex: Q23.MD39 Env trimer
      • Protein or peptide: Q23.MD39 Surface protein gp120
      • Protein or peptide: Q23.MD39 Transmembrane protein gp41
    • Complex: Fab 35O22
      • Protein or peptide: 35O22 Fab Heavy Chain
      • Protein or peptide: 35O22 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / Complex / 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: 3.19 Å
AuthorsLin ZJ / Cui J / Du J / Habib R / Kulp D / Pallesen J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2025
Title: Deep Mining of the Human Antibody Repertoire Identifies Frequent and Genetically Diverse CDRH3 Topologies Targetable by Vaccination.
Authors: Rumi Habib / Shahlo O Solieva / Zi Jie Lin / Sukanya Ghosh / Kelly Bayruns / Maya Singh / Colby J Agostino / Nicholas J Tursi / Kirsten J Sowers / Jinwei Huang / Ryan S Roark / Mansi Purwar ...Authors: Rumi Habib / Shahlo O Solieva / Zi Jie Lin / Sukanya Ghosh / Kelly Bayruns / Maya Singh / Colby J Agostino / Nicholas J Tursi / Kirsten J Sowers / Jinwei Huang / Ryan S Roark / Mansi Purwar / Younghoon Park / Kasirajan Ayyanathan / Hui Li / John W Carey / Amber Kim / Joyce Park / Madison E McCanna / Ashwin N Skelly / Neethu Chokkalingam / Sinja Kriete / Nicholas Shupin / Alana Huynh / Susanne Walker / Roopak Sadeesh / Niklas Laenger / Jianqiu Du / Jiayan Cui / Ami Patel / Amelia Escolano / Peter D Kwong / Lawrence Shapiro / Gregory R Bowman / Beatrice H Hahn / George M Shaw / David B Weiner / Jesper Pallesen / Daniel W Kulp
Abstract: Germline targeting vaccination strategies against highly variable pathogens such as HIV aim to elicit broadly neutralizing antibodies (bnAbs) with particular immunogenetic or structural features. The ...Germline targeting vaccination strategies against highly variable pathogens such as HIV aim to elicit broadly neutralizing antibodies (bnAbs) with particular immunogenetic or structural features. The V2 apex of the HIV Env protein is a promising target for a class of bnAbs that contain conserved structural motifs in the heavy chain complementarity determining region 3 (CDRH3). Here, we show that these structural motifs are targetable by vaccination by characterizing V2 apex 'axe-like' CDRH3s in the human repertoire and developing new immunogens capable of engaging them. We determined the frequency and diversity of axe-like CDHR3s in healthy human donors using a series of structural informatics approaches, finding these precursors in nearly 90% of donors. Axe-targeting immunogens based on the HIV Env Q23.17 bound axe-like precursors in cryo-EM structures, induced V2 apex-specific antibody responses in humanized mice, and induced axe-like heterologous neutralizing antibodies in rhesus macaques infected with a germline-targeted simian-human immunodeficiency virus. These results illustrate a new structure-guided immunoinformatic vaccine design paradigm that can be employed to elicit immunogenetically diverse yet structurally conserved classes of antibodies.
SIGNIFICANCE STATEMENT: Many broadly neutralizing antibodies (bnAbs) utilize modes of epitope recognition dominated by the antibody complementarity determining region 3 (CDRH3). The CDRH3 is the most ...SIGNIFICANCE STATEMENT: Many broadly neutralizing antibodies (bnAbs) utilize modes of epitope recognition dominated by the antibody complementarity determining region 3 (CDRH3). The CDRH3 is the most diverse part of the antibody, posing a challenge for germline targeting vaccine designs that aim to elicit antibodies with particular immunogenetic features. Vaccine design strategies that accommodate CDRH3 variability are therefore needed. Many HIV Env V2 apex bnAbs share "axe-like" CDRH3 microfolds that arise from diverse immunogenetic origins. Here we determined the frequency in humans of B cells with such CDRH3 topologies and designed immunogens to engage their precursors. This work opens a path toward vaccines that engage specific structural classes of B cells, thereby advancing the rational design of immunogens for HIV and other pathogens.
History
DepositionSep 5, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46914.png

Downloads & links

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Map

FileDownload / File: emd_46914.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 340 pix.
= 358.36 Å		1.05 Å/pix.
x 340 pix.
= 358.36 Å		1.05 Å/pix.
x 340 pix.
= 358.36 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.340558 - 4.4999733
Average (Standard dev.)0.00093228277 (±0.091998175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 358.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46914_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_46914_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Q23.MD39 Env trimer in Complex with 35O22

EntireName: Q23.MD39 Env trimer in Complex with 35O22
Components
  • Complex: Q23.MD39 Env trimer in Complex with 35O22
    • Complex: Q23.MD39 Env trimer
      • Protein or peptide: Q23.MD39 Surface protein gp120
      • Protein or peptide: Q23.MD39 Transmembrane protein gp41
    • Complex: Fab 35O22
      • Protein or peptide: 35O22 Fab Heavy Chain
      • Protein or peptide: 35O22 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Q23.MD39 Env trimer in Complex with 35O22

SupramoleculeName: Q23.MD39 Env trimer in Complex with 35O22 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Q23.MD39 Env trimer

SupramoleculeName: Q23.MD39 Env trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: Fab 35O22

SupramoleculeName: Fab 35O22 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Q23.MD39 Surface protein gp120

MacromoleculeName: Q23.MD39 Surface protein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.753762 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ENLWVTVYYG VPVWRDADTT LFCASDAKAY ETEKHNVWAT HACVPTDPNP QEIHLDNVTE KFNMWKNNMV EQMHEDIISL WDQSLKPCV KLTPLCVTLH CTNVTSVNTT GDREGLKNCS FNMTTELRDK RQKVYSLFYR LDIVPINENQ GSEYRLINCN T SAITQACP ...String:
ENLWVTVYYG VPVWRDADTT LFCASDAKAY ETEKHNVWAT HACVPTDPNP QEIHLDNVTE KFNMWKNNMV EQMHEDIISL WDQSLKPCV KLTPLCVTLH CTNVTSVNTT GDREGLKNCS FNMTTELRDK RQKVYSLFYR LDIVPINENQ GSEYRLINCN T SAITQACP KVSFEPIPIH YCTPAGFAIL KCKDEGFNGT GLCKNVSTVQ CTHGIKPVVS TQLLLNGSLA EKNIIIRSEN IT NNAKIII VQLVQPVTIK CIRPNNNTVK SIRIGPGQAF YYTGDIIGDI RQAHCNVTRS RWNKTLQEVA EKLRTYFGNK TII FAQSSG GDLEITTHSF NCGGEFFYCN TSGLFNSTWY VNSTWNDTDS TQESNDTITL PCRIKQIINM WQRAGQAMYA PPIP GVIKC ESNITGLLLT RDGGKDNNVN ETFRPGGSDM RDNWRSELYK YKVVEIEPLG VAPTRCKRRV VE

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Q23.MD39 Transmembrane protein gp41

MacromoleculeName: Q23.MD39 Transmembrane protein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.329604 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASITLTVQA RQLLSGIVQQ QNNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNKSLD EIWNNMTWLQ WDKEINNYTQ LIYRLIEESQ NQQEKNEKEL LELD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: 35O22 Fab Heavy Chain

MacromoleculeName: 35O22 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.170533 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QGQLVQSGAE LKKPGASVKI SCKTSGYRFN FYHINWIRQT AGRGPEWMGW ISPYSGDKNL APAFQDRVIM TTDTEVPVTS FTSTGAAYM EIRNLKFDDT GTYFCAKGLL RDGSSTWLPY LWGQGTLLTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV ...String:
QGQLVQSGAE LKKPGASVKI SCKTSGYRFN FYHINWIRQT AGRGPEWMGW ISPYSGDKNL APAFQDRVIM TTDTEVPVTS FTSTGAAYM EIRNLKFDDT GTYFCAKGLL RDGSSTWLPY LWGQGTLLTV SSASTKGPSV FPLAPSSKST SGGTAALGCL V KDYFPEPV TVSWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSCDKGL EV LFQ

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Macromolecule #4: 35O22 Fab Light Chain

MacromoleculeName: 35O22 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.318824 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQSASV SGSLGQSVTI SCTGPNSVCC SHKSISWYQW PPGRAPTLII YEDNERAPGI SPRFSGYKSY WSAYLTISDL RPEDETTYY CCSYTHNSGC VFGTGTKVSV LGQSKANPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSVLTQSASV SGSLGQSVTI SCTGPNSVCC SHKSISWYQW PPGRAPTLII YEDNERAPGI SPRFSGYKSY WSAYLTISDL RPEDETTYY CCSYTHNSGC VFGTGTKVSV LGQSKANPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 19 / 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

Concentration0.07 mg/mL
BufferpH: 7.6 / Details: 1X PBS
GridModel: Au-flat 1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 150988
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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