[English] 日本語
Yorodumi
- EMDB-26586: Negative stain EM map of Y2 COBRA hemagglutinin in complex with m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26586
TitleNegative stain EM map of Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05
Map dataNegative stain EM map of Y2 COBRA hemagglutinin binding monoclonal antibody P1-05
Sample
  • Complex: Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05
    • Complex: Y2 COBRA hemagglutinin
    • Complex: P1-05 monoclonal antibody
Biological speciesCricetulus griseus (Chinese hamster)
Methodsingle particle reconstruction / negative staining / Resolution: 11.0 Å
AuthorsHan J / Dzimianski JV / DuBois RM / Ward A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: J Immunol / Year: 2022
Title: The Pre-Existing Human Antibody Repertoire to Computationally Optimized Influenza H1 Hemagglutinin Vaccines.
Authors: Kaito Nagashima / John V Dzimianski / Julianna Han / Nada Abbadi / Aaron D Gingerich / Fredejah Royer / Sara O'Rourke / Giuseppe A Sautto / Ted M Ross / Andrew B Ward / Rebecca M DuBois / Jarrod J Mousa /
Abstract: Computationally optimized broadly reactive Ag (COBRA) hemagglutinin (HA) immunogens have previously been generated for several influenza subtypes to improve vaccine-elicited Ab breadth. As nearly all ...Computationally optimized broadly reactive Ag (COBRA) hemagglutinin (HA) immunogens have previously been generated for several influenza subtypes to improve vaccine-elicited Ab breadth. As nearly all individuals have pre-existing immunity to influenza viruses, influenza-specific memory B cells will likely be recalled upon COBRA HA vaccination. We determined the epitope specificity and repertoire characteristics of pre-existing human B cells to H1 COBRA HA Ags. Cross-reactivity between wild-type HA and H1 COBRA HA proteins P1, X6, and Y2 were observed for isolated mAbs. The mAbs bound five distinct epitopes on the pandemic A/California/04/2009 HA head and stem domains, and most mAbs had hemagglutination inhibition and neutralizing activity against 2009 pandemic H1 strains. Two head-directed mAbs, CA09-26 and CA09-45, had hemagglutination inhibition and neutralizing activity against a prepandemic H1 strain. One mAb, P1-05, targeted the stem region of H1 HA, but did not compete with a known stem-targeting H1 mAb. We determined that mAb P1-05 recognizes a recently discovered HA epitope, the anchor epitope, and we identified similar mAbs using B cell repertoire sequencing. In addition, the trimerization domain distance from HA was critical to recognition of this epitope by mAb P1-05, suggesting the importance of protein design for vaccine formulations. Overall, these data indicate that seasonally vaccinated individuals possess a population of functional H1 COBRA HA-reactive B cells that target head, central stalk, and anchor epitopes, and they demonstrate the importance of structure-based assessment of subunit protein vaccine candidates to ensure accessibility of optimal protein epitopes.
History
DepositionApr 1, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateJul 13, 2022-
Current statusJul 13, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26586.png

Downloads & links

-
Map

FileDownload / File: emd_26586.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of Y2 COBRA hemagglutinin binding monoclonal antibody P1-05
Voxel sizeX=Y=Z: 1.98 Å
Density
Contour LevelBy AUTHOR: 1.4
Minimum - Maximum-0.470915 - 3.3580077
Average (Standard dev.)-0.0244092 (±0.26363954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 356.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Negative stain EM half map A of Y2...

Fileemd_26586_half_map_1.map
AnnotationNegative stain EM half map A of Y2 COBRA hemagglutinin binding monoclonal antibody P1-05
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Negative stain EM half map B of Y2...

Fileemd_26586_half_map_2.map
AnnotationNegative stain EM half map B of Y2 COBRA hemagglutinin binding monoclonal antibody P1-05
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05

EntireName: Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05
Components
  • Complex: Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05
    • Complex: Y2 COBRA hemagglutinin
    • Complex: P1-05 monoclonal antibody

-
Supramolecule #1: Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05

SupramoleculeName: Y2 COBRA hemagglutinin in complex with monoclonal antibody P1-05
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Cricetulus griseus (Chinese hamster) / Organ: ovaries
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant cell: CHO

-
Supramolecule #2: Y2 COBRA hemagglutinin

SupramoleculeName: Y2 COBRA hemagglutinin / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Details: HA antigen based on A/California/04/2009 H1N1 HA
Source (natural)Organism: Cricetulus griseus (Chinese hamster) / Organ: ovaries
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant cell: CHO

-
Supramolecule #3: P1-05 monoclonal antibody

SupramoleculeName: P1-05 monoclonal antibody / type: complex / Chimera: Yes / ID: 3 / Parent: 1
Source (natural)Organism: Cricetulus griseus (Chinese hamster) / Organ: ovaries
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant cell: CHO

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
StainingType: NEGATIVE / Material: uranyl formate / Details: 2% w/v
GridModel: Homemade / Pretreatment - Type: PLASMA CLEANING

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.0 µm
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

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

4m4y

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12717

+
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