[English] 日本語
Yorodumi
- EMDB-43909: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43909
TitlensEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463)
Map data
Sample
  • Complex: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463)
    • Complex: Rabbit Polyclonal Antibody - N611/N625, V2, C3/V5 and Base Epitopes
      • Protein or peptide: HIV-1 16055 SOSIP.v8.3 - gp140
    • Complex: HIV-1 16055 SOSIP.v8.3 Env
KeywordsHIV / Polyclonal / Antibodies / nsEMPEM / Rabbit / VIRAL PROTEIN
Biological speciesOryctolagus cuniculus (rabbit) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 Å
AuthorsBrown S / Antansijevic A / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136621 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Sci Immunol / Year: 2025
Title: Anti-immune complex antibodies are elicited during repeated immunization with HIV Env immunogens.
Authors: Sharidan Brown / Aleksandar Antanasijevic / Leigh M Sewall / Daniel Montiel Garcia / James Ferguson / Philip J M Brouwer / Rogier W Sanders / Andrew B Ward /
Abstract: Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody ...Vaccination strategies against HIV-1 aim to elicit broadly neutralizing antibodies (bnAbs) using prime-boost regimens with HIV envelope (Env) immunogens. Epitope mapping has shown that early antibody responses are directed to easily accessible nonneutralizing epitopes on Env instead of bnAb epitopes. Autologously neutralizing antibody responses appear upon boosting, once immunodominant epitopes are saturated. Here, we use electron microscopy-based polyclonal epitope mapping (EMPEM) to elucidate how repeated immunization with HIV Env SOSIP immunogens results in the generation of Ab2α anti-idiotypic antibodies in rabbits and rhesus macaques. We present the structures of six anti-immune complex antibodies and find that they target idiotopes composed of framework regions of antibodies bound to Env. Examination of cryo-electron microscopy density enabled prediction of sequences for an anti-immune complex antibody, the paratope of which is enriched with aromatic amino acids. This work sheds light on current vaccine development efforts for HIV, as well as for other pathogens in which repeated exposure to antigen is required.
History
DepositionMar 4, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43909.png

Downloads & links

-
Map

FileDownload / File: emd_43909.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 224 pix.
= 396.48 Å		1.77 Å/pix.
x 224 pix.
= 396.48 Å		1.77 Å/pix.
x 224 pix.
= 396.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.019
Minimum - Maximum-0.047187015 - 0.078447975
Average (Standard dev.)-0.00007501324 (±0.003880626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 396.47998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Additional Map 1 - V2 and Base Epitopes

Fileemd_43909_additional_1.map
AnnotationAdditional Map 1 - V2 and Base Epitopes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Additional Map 2 - C3/V5 and V2 Epitopes

Fileemd_43909_additional_2.map
AnnotationAdditional Map 2 - C3/V5 and V2 Epitopes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43909_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43909_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N...

EntireName: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463)
Components
  • Complex: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463)
    • Complex: Rabbit Polyclonal Antibody - N611/N625, V2, C3/V5 and Base Epitopes
      • Protein or peptide: HIV-1 16055 SOSIP.v8.3 - gp140
    • Complex: HIV-1 16055 SOSIP.v8.3 Env

-
Supramolecule #1: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N...

SupramoleculeName: nsEM of HIV-1 16055 SOSIP.v8.3 Env in Complex with Week 22 N611/N625, V2, C3/V5 and Base Epitope pAbs (Rabbit ID: 2463)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

-
Supramolecule #2: Rabbit Polyclonal Antibody - N611/N625, V2, C3/V5 and Base Epitopes

SupramoleculeName: Rabbit Polyclonal Antibody - N611/N625, V2, C3/V5 and Base Epitopes
type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Details: Main Map - N611/N625 and V2 Epitopes Additional Map 1 - V2 and Base Epitopes Additional Map 2 - C3/V5 and V2 Epitopes
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

-
Supramolecule #3: HIV-1 16055 SOSIP.v8.3 Env

SupramoleculeName: HIV-1 16055 SOSIP.v8.3 Env / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Human immunodeficiency virus 1

-
Macromolecule #1: HIV-1 16055 SOSIP.v8.3 - gp140

MacromoleculeName: HIV-1 16055 SOSIP.v8.3 - gp140 / type: protein_or_peptide / ID: 1 / Details: The sequence contains engineered SOSIP mutations. / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARNGNLW VTVYYGVPVW KDAETTLFCA SDAKAYEKEK RNVWATHCCV PTDPNPQEMV LENVTENFNM WKNDMVEQMH EDVISLWDQS LKPCVKLTPL CVTLECRQVN TTNATSSVNV TNGEEIKNCS FNATTELRDK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARNGNLW VTVYYGVPVW KDAETTLFCA SDAKAYEKEK RNVWATHCCV PTDPNPQEMV LENVTENFNM WKNDMVEQMH EDVISLWDQS LKPCVKLTPL CVTLECRQVN TTNATSSVNV TNGEEIKNCS FNATTELRDK KQKVYALFYR LDIVPLEEER KGNSSKYRLI NCNTSAITQA CPKVTFDPIP IHYCAPAGYA ILKCNNKTFN GTGPCNNVST VQCTHGIKPV VSTQLLLNGS LAEGEIIIRS ENLTNNVKTI IVHLNESVEI VCTRPNNNTV KSIRIGPGQW FYYTGDIIGN IRQAYCNIKK DDWIRTLQRV GKKLAEHFPR RIINFTQPAG GDLEITTHSF NCRGEFFYCN TSSLFNSTYN PNDTNSNSSS SNSSLDITIP CRIKQIINMW QRVGQAMYAP PIEGNITCKS NITGLLLVRD GGVESNETEI FRPGGGDMRN NWRSELYKYK VVEIKPLGIA PTRCKRRVVE RRRRRRAVGL GAVSFGFLGA AGSTMGAASI TLTVQARQLL SGIVQQQSNL LKAPECQQHL LQDGHWGIKQ LQTRVLAIEH YLKDQQLLGI WGCSGKLICC TAVPWNSSWS NKSHDEIWGN MTWMQWDREI SNYTNTIYRL LEDSQNQQEQ NEKDLLALD

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING

-
Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
EMDB ID:

20396


Details: Low pass filtered to 40 angstroms.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0)
Details: Number of particles used for the final reconstruction of Additional Map 1 (2381) and Additional Map 2 (2027).
Number images used: 2557
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://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