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- EMDB-73961: CK52.1 Fab in complex with Q23.RH-GT. Env -

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Basic information

Entry
Database: EMDB / ID: EMD-73961
TitleCK52.1 Fab in complex with Q23.RH-GT. Env
Map data
Sample
  • Complex: CK52.1 Fab in complex with Q23.RH-GT. Env
    • Complex: CK52.1 Fab
    • Complex: Q23.RH-GT Env
    • Complex: VRC01 Fab
    • Complex: 35O22 Fab
KeywordsAntibody / Complex / HIV-1 Env / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 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.USA / Year: 2026
Title: Deep Mining of the Human Antibody Repertoire Identifies Frequent and Genetically Diverse CDRH3 Topologies Targetable by Vaccination
Authors: Habib R / Solieva SO / Lin ZJ / Ghosh S / Bayruns K / Singh M / Agostino CJ / Tursi NJ / Sowers KJ / Huang J / Roark RS / Purwar M / Park Y / Ayyanathan K / Li H / Carey JW / Kim A / Park J ...Authors: Habib R / Solieva SO / Lin ZJ / Ghosh S / Bayruns K / Singh M / Agostino CJ / Tursi NJ / Sowers KJ / Huang J / Roark RS / Purwar M / Park Y / Ayyanathan K / Li H / Carey JW / Kim A / Park J / McCanna ME / Skelly AN / Chokkalingam N / Kriete S / Shupin N / Huynh A / Walker S / Sadeesh R / Laenger N / Du J / Cui J / Patel A / Escolano A / Kwong PD / Shapiro L / Bowman GR / Hahn BH / Shaw GM / Weiner DB / Pallesen J / Kulp DW
History
DepositionNov 18, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73961.png

Downloads & links

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Map

FileDownload / File: emd_73961.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 512 pix.
= 357.12 Å		0.7 Å/pix.
x 512 pix.
= 357.12 Å		0.7 Å/pix.
x 512 pix.
= 357.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6975 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-0.15712191 - 15.622469000000001
Average (Standard dev.)-0.039987627 (±0.45984983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 357.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_73961_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_73961_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 : CK52.1 Fab in complex with Q23.RH-GT. Env

EntireName: CK52.1 Fab in complex with Q23.RH-GT. Env
Components
  • Complex: CK52.1 Fab in complex with Q23.RH-GT. Env
    • Complex: CK52.1 Fab
    • Complex: Q23.RH-GT Env
    • Complex: VRC01 Fab
    • Complex: 35O22 Fab

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Supramolecule #1: CK52.1 Fab in complex with Q23.RH-GT. Env

SupramoleculeName: CK52.1 Fab in complex with Q23.RH-GT. Env / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: CryoEMPEM of Q23.RH-GT in complex with Rhesus macaque CK52 serum at week 24.

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Supramolecule #2: CK52.1 Fab

SupramoleculeName: CK52.1 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: Identified V2 apex antibody from CK52 week 24 serum
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #3: Q23.RH-GT Env

SupramoleculeName: Q23.RH-GT Env / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 / Details: Engineered HIV-1 Env Q23.RH-GT
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #4: VRC01 Fab

SupramoleculeName: VRC01 Fab / type: complex / ID: 4 / Parent: 1 / Details: HIV-1 Env Antibody VRC01 Fab
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: 35O22 Fab

SupramoleculeName: 35O22 Fab / type: complex / ID: 5 / Parent: 1 / Details: HIV-1 Env antibody 35O22 Fab
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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 71460
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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