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- EMDB-36815: Recognition determinants of broad and potent HIV-1 neutralization... -

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Entry
Database: EMDB / ID: EMD-36815
TitleRecognition determinants of broad and potent HIV-1 neutralization by an affinity matured antibody from a pediatric elite-neutralizer
Map data44m Fab complex with HIV BG505.SOSIP envelope trimer
Sample
  • Complex: BG505 SOSIP trimer in complex with 44m bnAb
    • Complex: BG505 SOSIP trimer
      • Complex: AIIMS 44m
KeywordsA monoclonal antibody / HIV Trimer / Cryo-EM single particle / Structural analysis / ANTIVIRAL PROTEIN / VIRAL PROTEIN-ANTIVIRAL PROTEIN complex
Biological speciesHIV-1 06TG.HT032 (virus) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsKumar S / Singh S / Chatterjee A / Bajpai P / Sharma S / Katpara S / Lodha R / Dutta S / Luthra K
Funding support India, 6 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR2450/MED/29/1222/2017 India
Department of Biotechnology (DBT, India)BT/PR30120/MED/29/1339/2018 India
Department of Biotechnology (DBT, India)BT/INF/22/SP22/844/2107 India
Department of Science & Technology (DST, India)SR/FST/LSII-039/2015 India
Science and Engineering Research Board (SERB)SERB-EMR/2016/000608, SERB-IPA/2020/000094 India
Department of Biotechnology (DBT, India)IA/E/18/1/504307 India
Citation
Journal: iScience / Year: 2023
Title: Recognition determinants of improved HIV-1 neutralization by a heavy chain matured pediatric antibody.
Authors: Sanjeev Kumar / Swarandeep Singh / Arnab Chatterjee / Prashant Bajpai / Shaifali Sharma / Sanket Katpara / Rakesh Lodha / Somnath Dutta / Kalpana Luthra /
Abstract: The structural and characteristic features of HIV-1 broadly neutralizing antibodies (bnAbs) from chronically infected pediatric donors are currently unknown. Herein, we characterized a heavy chain ...The structural and characteristic features of HIV-1 broadly neutralizing antibodies (bnAbs) from chronically infected pediatric donors are currently unknown. Herein, we characterized a heavy chain matured HIV-1 bnAb 44m, identified from a pediatric elite-neutralizer. Interestingly, in comparison to its wild-type AIIMS-P01 bnAb, 44m exhibited moderately higher level of somatic hypermutations of 15.2%. The 44m neutralized 79% of HIV-1 heterologous viruses (n = 58) tested, with a geometric mean IC titer of 0.36 μg/mL. The cryo-EM structure of 44m Fab in complex with fully cleaved glycosylated native-like BG505.SOSIP.664.T332N gp140 envelope trimer at 4.4 Å resolution revealed that 44m targets the V3-glycan N332-supersite and GDIR motif to neutralize HIV-1 with improved potency and breadth, plausibly attributed by a matured heavy chain as compared to that of wild-type AIIMS-P01. This study further improves our understanding on pediatric HIV-1 bnAbs and structural basis of broad HIV-1 neutralization by 44m may be useful blueprint for vaccine design in future.
#1: Journal: To Be Published
Title: Recognition determinants of broad and potent HIV-1 neutralization by an affinity matured antibody from a pediatric elite-neutralizer
Authors: Kumar S / Singh S / Chatterjee A / Bajpai P / Sharma S / Katpara S / Lodha R / Dutta S / Luthra K
History
DepositionJul 11, 2023-
Header (metadata) releaseJun 19, 2024-
Map releaseJun 19, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36815.png

Downloads & links

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Map

FileDownload / File: emd_36815.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation44m Fab complex with HIV BG505.SOSIP envelope trimer
Voxel sizeX=Y=Z: 1.17 Å
Density
Contour LevelBy AUTHOR: 0.0092
Minimum - Maximum-0.04160788 - 0.0756906
Average (Standard dev.)-0.000011486186 (±0.002607925)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 327.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_36815_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_36815_half_map_2.map
Annotationhalf 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 : BG505 SOSIP trimer in complex with 44m bnAb

EntireName: BG505 SOSIP trimer in complex with 44m bnAb
Components
  • Complex: BG505 SOSIP trimer in complex with 44m bnAb
    • Complex: BG505 SOSIP trimer
      • Complex: AIIMS 44m

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Supramolecule #1: BG505 SOSIP trimer in complex with 44m bnAb

SupramoleculeName: BG505 SOSIP trimer in complex with 44m bnAb / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1

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Supramolecule #2: BG505 SOSIP trimer

SupramoleculeName: BG505 SOSIP trimer / type: complex / ID: 2 / Parent: 1 / Details: HIV-1 trimer
Source (natural)Organism: HIV-1 06TG.HT032 (virus)

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Supramolecule #3: AIIMS 44m

SupramoleculeName: AIIMS 44m / type: complex / ID: 3 / Parent: 2 / Details: monoclonal antibody
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

Concentration1.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219374
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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