[English] 日本語
Yorodumi
- EMDB-36815: Recognition determinants of broad and potent HIV-1 neutralization... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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

-
Structure visualization

Supplemental images

emd_36815.png

Downloads & links

-
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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 280 pix.
= 327.6 Å		1.17 Å/pix.
x 280 pix.
= 327.6 Å		1.17 Å/pix.
x 280 pix.
= 327.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
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)

-
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)

-
Sample components

-
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

-
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

-
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)

-
Supramolecule #3: AIIMS 44m

SupramoleculeName: AIIMS 44m / type: complex / ID: 3 / Parent: 2 / Details: monoclonal antibody
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more