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- EMDB-73950: CryoEM map of CK52.1 in complex with Q23.V033GT -

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Basic information

Entry
Database: EMDB / ID: EMD-73950
TitleCryoEM map of CK52.1 in complex with Q23.V033GT
Map data
Sample
  • Complex: Q23.V033GT Env trimer in complex with a CK52.1 Fab
    • Complex: Q23.V033GT Env trimer
    • Complex: CK52.1 Fab
KeywordsAntibody / Complex / HIV-1 Env / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.17 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: Proc Natl Acad Sci U S A / Year: 2026
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 immunogens capable of engaging them. We determined the frequency and diversity of axe-like CDRH3s 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-electron microscopy 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-HIV. These results illustrate a structure-guided immunoinformatic vaccine design paradigm that can be employed to elicit immunogenetically diverse yet structurally conserved classes of antibodies.
History
DepositionNov 18, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73950.png

Downloads & links

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Map

FileDownload / File: emd_73950.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å		0.95 Å/pix.
x 400 pix.
= 380. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0849
Minimum - Maximum-0.37149978 - 0.6282819
Average (Standard dev.)-0.0001995411 (±0.012407175)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 380.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_73950_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_73950_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 : Q23.V033GT Env trimer in complex with a CK52.1 Fab

EntireName: Q23.V033GT Env trimer in complex with a CK52.1 Fab
Components
  • Complex: Q23.V033GT Env trimer in complex with a CK52.1 Fab
    • Complex: Q23.V033GT Env trimer
    • Complex: CK52.1 Fab

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Supramolecule #1: Q23.V033GT Env trimer in complex with a CK52.1 Fab

SupramoleculeName: Q23.V033GT Env trimer in complex with a CK52.1 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: CryoEMPEM of Q23.V033GT Env trimer with Fabs isolated from Rhesus macaque CK52 serum at week 24

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Supramolecule #2: Q23.V033GT Env trimer

SupramoleculeName: Q23.V033GT 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: CK52.1 Fab

SupramoleculeName: CK52.1 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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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: 7.6 / Details: 1X PBS
GridModel: UltrAuFoil R1.2/1.3 / 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 GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 165144
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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