[English] 日本語
Yorodumi
- EMDB-41542: Polyclonal immune complex of Fab binding the H2 HA from serum of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41542
TitlePolyclonal immune complex of Fab binding the H2 HA from serum of subject 3-3 at week 4
Map dataNegative stain map of global refinement of particle stack used to sort polyclonal responses to H2 HA from human subject 3-3 at week 4
Sample
  • Complex: Polyclonal immune complex of Fab binding the H2 HA from serum of subject 3-3 at week 4
Keywordsinfluenza / hemagglutinin / H2 / polyclonal complex / Fab complex / viral fusion protein / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsYang YR / Han J / Richey ST / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: To Be Published
Title: Mapping HA epitopes targeted by polyclonal antibodies following H2N2 vaccination in humans
Authors: Yang YR / Han J / Perrett HR / Richey ST / Jackson AM / Rodriguez AJ / Gillespie RA / O'Connell S / Raab JE / Cominsky LY / Chopde A / Kanekiyo M / Houser KV / Chen GL / McDermott AB / Andrews SF / Ward AB
History
DepositionAug 8, 2023-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41542.png

Downloads & links

-
Map

FileDownload / File: emd_41542.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain map of global refinement of particle stack used to sort polyclonal responses to H2 HA from human subject 3-3 at week 4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 160 pix.
= 329.6 Å		2.06 Å/pix.
x 160 pix.
= 329.6 Å		2.06 Å/pix.
x 160 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0214
Minimum - Maximum-0.037549086 - 0.11915722
Average (Standard dev.)-0.00007058204 (±0.0043569934)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_41542_additional_1.map
AnnotationNegative stain map of polyclonal Fab binding the H2 HA central stem epitope from human subject 3-3 at week 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_41542_additional_2.map
AnnotationNegative stain map of polyclonal Fab binding the H2 HA RBS epitope from human subject 3-3 at week 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Negative stain map of half map A for...

Fileemd_41542_half_map_1.map
AnnotationNegative stain map of half map A for global refinement of particle stack used to sort polyclonal responses to H2 HA from human subject 3-3 at week 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Negative stain map of half map B for...

Fileemd_41542_half_map_2.map
AnnotationNegative stain map of half map B for global refinement of particle stack used to sort polyclonal responses to H2 HA from human subject 3-3 at week 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Polyclonal immune complex of Fab binding the H2 HA from serum of ...

EntireName: Polyclonal immune complex of Fab binding the H2 HA from serum of subject 3-3 at week 4
Components
  • Complex: Polyclonal immune complex of Fab binding the H2 HA from serum of subject 3-3 at week 4

-
Supramolecule #1: Polyclonal immune complex of Fab binding the H2 HA from serum of ...

SupramoleculeName: Polyclonal immune complex of Fab binding the H2 HA from serum of subject 3-3 at week 4
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.015 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: 2% w/v uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

+
Image processing

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

3ku5

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 27331
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

+
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://pdbjlc1.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