[English] 日本語
Yorodumi
- EMDB-46646: HIV-1 BaL Env in complex with CD4 mimetic CJF-III-288 and 17b IgG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46646
TitleHIV-1 BaL Env in complex with CD4 mimetic CJF-III-288 and 17b IgG
Map dataPrimary map made from recombining two half maps with relion_postprocess
Sample
  • Virus: Human immunodeficiency virus 1
KeywordsEnv / IgG / CD4mc / HIV-1 / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 21.5 Å
AuthorsGrunst MW
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37AI150560 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI176904 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI150471 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31AI176650 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32 AI055403 United States
CitationJournal: bioRxiv / Year: 2024
Title: The asymmetric opening of HIV-1 Env by a potent CD4 mimetic enables anti-coreceptor binding site antibodies to mediate ADCC.
Authors: Jonathan Richard / Michael W Grunst / Ling Niu / Marco A Díaz-Salinas / William D Tolbert / Lorie Marchitto / Fei Zhou / Catherine Bourassa / Derek Yang / Ta Jung Chiu / Hung-Ching Chen / ...Authors: Jonathan Richard / Michael W Grunst / Ling Niu / Marco A Díaz-Salinas / William D Tolbert / Lorie Marchitto / Fei Zhou / Catherine Bourassa / Derek Yang / Ta Jung Chiu / Hung-Ching Chen / Mehdi Benlarbi / / Suneetha Gottumukkala / Wenwei Li / Katrina Dionne / Étienne Bélanger / Debashree Chatterjee / Halima Medjahed / Wayne A Hendrickson / Joseph Sodroski / Zabrina C Lang / Abraham J Morton / Rick K Huang / Doreen Matthies / Amos B Smith / Walther Mothes / James B Munro / Marzena Pazgier / Andrés Finzi /
Abstract: HIV-1 envelope glycoproteins (Env) from primary HIV-1 isolates typically adopt a pretriggered "closed" conformation that resists to CD4-induced (CD4i) non-neutralizing antibodies (nnAbs) mediating ...HIV-1 envelope glycoproteins (Env) from primary HIV-1 isolates typically adopt a pretriggered "closed" conformation that resists to CD4-induced (CD4i) non-neutralizing antibodies (nnAbs) mediating antibody-dependent cellular cytotoxicity (ADCC). CD4-mimetic compounds (CD4mcs) "open-up" Env allowing binding of CD4i nnAbs, thereby sensitizing HIV-1-infected cells to ADCC. Two families of CD4i nnAbs, the anti-cluster A and anti-coreceptor binding site (CoRBS) Abs, are required to mediate ADCC in combination with the indane CD4mc BNM-III-170. Recently, new indoline CD4mcs with improved potency and breadth have been described. Here, we show that the lead indoline CD4mc, CJF-III-288, sensitizes HIV-1-infected cells to ADCC mediated by anti-CoRBS Abs alone, contributing to improved ADCC activity. Structural and conformational analyses reveal that CJF-III-288, in combination with anti-CoRBS Abs, potently stabilizes an asymmetric "open" State-3 Env conformation, This Env conformation orients the anti-CoRBS Ab to improve ADCC activity and therapeutic potential.
History
DepositionAug 20, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46646.png

Downloads & links

-
Map

FileDownload / File: emd_46646.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map made from recombining two half maps with relion_postprocess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.69 Å/pix.
x 112 pix.
= 301.504 Å		2.69 Å/pix.
x 112 pix.
= 301.504 Å		2.69 Å/pix.
x 112 pix.
= 301.504 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.692 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 140.0
Minimum - Maximum-117.721869999999996 - 357.344359999999995
Average (Standard dev.)17.43805 (±39.163756999999997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions112112112
Spacing112112112
CellA=B=C: 301.504 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_46646_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: HalfMap of 1696 particles generated using PEET

Fileemd_46646_half_map_1.map
AnnotationHalfMap of 1696 particles generated using PEET
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: HalfMap of 1811 particles generated using PEET

Fileemd_46646_half_map_2.map
AnnotationHalfMap of 1811 particles generated using PEET
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Human immunodeficiency virus 1

EntireName: Human immunodeficiency virus 1
Components
  • Virus: Human immunodeficiency virus 1

-
Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Sci species strain: BaL / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.0 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET / Number subtomograms used: 3507
ExtractionNumber tomograms: 84 / Number images used: 9419 / Reference model: Formless Blob on Membrane
Details: PEET program spikeInit was used to generate an initial reference.
Final 3D classificationSoftware - Name: PEET
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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://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