[English] 日本語
Yorodumi
- EMDB-27600: BG505 MD39 SOSIP in complex with Rh.L614 wk13 base, N335/N289, V5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27600
TitleBG505 MD39 SOSIP in complex with Rh.L614 wk13 base, N335/N289, V5/C3 and N611 epitope pAbs
Map dataRh.L614 wk13 base, N335/N289 and N611 pAbs (main map)
Sample
  • Complex: BG505 MD39 SOSIP in complex with Rh.L614 wk13 base, N335/N289, and N611 epitope pAbs
    • Complex: Rh.L614 wk13 base, N335/N289, and N611 epitope pAbs
    • Complex: BG505 MD39 SOSIP
Keywordspolyclonal antibodies / HIV-1 / Env / non-human primate / VIRAL PROTEIN
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsSewall LM / Richey ST / Ozorowski G / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144462 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Nature / Year: 2022
Title: Long-primed germinal centres with enduring affinity maturation and clonal migration.
Authors: Jeong Hyun Lee / Henry J Sutton / Christopher A Cottrell / Ivy Phung / Gabriel Ozorowski / Leigh M Sewall / Rebecca Nedellec / Catherine Nakao / Murillo Silva / Sara T Richey / Jonathan L ...Authors: Jeong Hyun Lee / Henry J Sutton / Christopher A Cottrell / Ivy Phung / Gabriel Ozorowski / Leigh M Sewall / Rebecca Nedellec / Catherine Nakao / Murillo Silva / Sara T Richey / Jonathan L Torres / Wen-Hsin Lee / Erik Georgeson / Michael Kubitz / Sam Hodges / Tina-Marie Mullen / Yumiko Adachi / Kimberly M Cirelli / Amitinder Kaur / Carolina Allers / Marissa Fahlberg / Brooke F Grasperge / Jason P Dufour / Faith Schiro / Pyone P Aye / Oleksandr Kalyuzhniy / Alessia Liguori / Diane G Carnathan / Guido Silvestri / Xiaoying Shen / David C Montefiori / Ronald S Veazey / Andrew B Ward / Lars Hangartner / Dennis R Burton / Darrell J Irvine / William R Schief / Shane Crotty /
Abstract: Germinal centres are the engines of antibody evolution. Here, using human immunodeficiency virus (HIV) Env protein immunogen priming in rhesus monkeys followed by a long period without further ...Germinal centres are the engines of antibody evolution. Here, using human immunodeficiency virus (HIV) Env protein immunogen priming in rhesus monkeys followed by a long period without further immunization, we demonstrate germinal centre B (B) cells that last for at least 6 months. A 186-fold increase in B cells was present by week 10 compared with conventional immunization. Single-cell transcriptional profiling showed that both light- and dark-zone germinal centre states were sustained. Antibody somatic hypermutation of B cells continued to accumulate throughout the 29-week priming period, with evidence of selective pressure. Env-binding B cells were still 49-fold above baseline at 29 weeks, which suggests that they could remain active for even longer periods of time. High titres of HIV-neutralizing antibodies were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing considerable immunodominance challenges for B cells. Memory B cells generated under these long priming conditions had higher levels of antibody somatic hypermutation, and both memory B cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous B cell lineage phylogenies spanning more than the 6-month germinal centre period were identified, demonstrating continuous germinal centre activity and selection for at least 191 days with no further antigen exposure. A long-prime, slow-delivery (12 days) immunization approach holds promise for difficult vaccine targets and suggests that patience can have great value for tuning of germinal centres to maximize antibody responses.
History
DepositionJul 13, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27600.png

Downloads & links

-
Map

FileDownload / File: emd_27600.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRh.L614 wk13 base, N335/N289 and N611 pAbs (main map)
Voxel sizeX=Y=Z: 1.77 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.04357271 - 0.100109324
Average (Standard dev.)0.0006952707 (±0.007012141)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 339.84 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Rh.L614 wk13 V5/C3 pAb (additional map 1)

Fileemd_27600_additional_1.map
AnnotationRh.L614 wk13 V5/C3 pAb (additional map 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Rh.L614 wk13 base, N335/N289 and N611 pAbs (half map 1)

Fileemd_27600_half_map_1.map
AnnotationRh.L614 wk13 base, N335/N289 and N611 pAbs (half map 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Rh.L614 wk13 base, N335/N289 and N611 pAbs (half map 2)

Fileemd_27600_half_map_2.map
AnnotationRh.L614 wk13 base, N335/N289 and N611 pAbs (half map 2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : BG505 MD39 SOSIP in complex with Rh.L614 wk13 base, N335/N289, an...

EntireName: BG505 MD39 SOSIP in complex with Rh.L614 wk13 base, N335/N289, and N611 epitope pAbs
Components
  • Complex: BG505 MD39 SOSIP in complex with Rh.L614 wk13 base, N335/N289, and N611 epitope pAbs
    • Complex: Rh.L614 wk13 base, N335/N289, and N611 epitope pAbs
    • Complex: BG505 MD39 SOSIP

-
Supramolecule #1: BG505 MD39 SOSIP in complex with Rh.L614 wk13 base, N335/N289, an...

SupramoleculeName: BG505 MD39 SOSIP in complex with Rh.L614 wk13 base, N335/N289, and N611 epitope pAbs
type: complex / ID: 1 / Parent: 0

-
Supramolecule #2: Rh.L614 wk13 base, N335/N289, and N611 epitope pAbs

SupramoleculeName: Rh.L614 wk13 base, N335/N289, and N611 epitope pAbs / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

-
Supramolecule #3: BG505 MD39 SOSIP

SupramoleculeName: BG505 MD39 SOSIP / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Human immunodeficiency virus 1

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl formate

-
Electron microscopy

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

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 3148

+
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