[English] 日本語
Yorodumi
- EMDB-9029: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9029
TitleHemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84
Map dataHemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84
Sample
  • Complex: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84.
    • Complex: Hemagglutinin trimeric ectodomain
    • Complex: Fab from IgG CR9114
    • Complex: Single-domain antibody SD84
Biological speciesInfluenza B virus (B/Massachusetts/02/2012) / Homo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsPallesen J / Nieusma T / Hoffman RMB / Ward AB
CitationJournal: Science / Year: 2018
Title: Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin.
Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut ...Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut Kolfschoten / David Zuijdgeest / Roel Straetemans / Ryan M B Hoffman / Travis Nieusma / Jesper Pallesen / Hannah L Turner / Steffen M Bernard / Andrew B Ward / Jinquan Luo / Leo L M Poon / Anna P Tretiakova / James M Wilson / Maria P Limberis / Ronald Vogels / Boerries Brandenburg / Joost A Kolkman / Ian A Wilson /
Abstract: Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza ...Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens.
History
DepositionAug 8, 2018-
Header (metadata) releaseSep 5, 2018-
Map releaseNov 14, 2018-
UpdateNov 14, 2018-
Current statusNov 14, 2018Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9029.png

Downloads & links

-
Map

FileDownload / File: emd_9029.map.gz / Format: CCP4 / Size: 45.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 228 pix.
= 298.68 Å		1.31 Å/pix.
x 228 pix.
= 298.68 Å		1.31 Å/pix.
x 228 pix.
= 298.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.018618532 - 0.07016123
Average (Standard dev.)0.00028470787 (±0.0036746194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions228228228
Spacing228228228
CellA=B=C: 298.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z228228228
origin x/y/z0.0000.0000.000
length x/y/z298.680298.680298.680
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS228228228
D min/max/mean-0.0190.0700.000

-
Supplemental data

-
Half map: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab...

Fileemd_9029_half_map_1.map
AnnotationHemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84, half map #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab...

Fileemd_9029_half_map_2.map
AnnotationHemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84, half map #2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in co...

EntireName: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84.
Components
  • Complex: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84.
    • Complex: Hemagglutinin trimeric ectodomain
    • Complex: Fab from IgG CR9114
    • Complex: Single-domain antibody SD84

-
Supramolecule #1: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in co...

SupramoleculeName: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in complex with Fab from IgG CR9114 and single-domain antibody SD84.
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 400 KDa

-
Supramolecule #2: Hemagglutinin trimeric ectodomain

SupramoleculeName: Hemagglutinin trimeric ectodomain / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Influenza B virus (B/Massachusetts/02/2012) / Strain: (B/Massachusetts/02/2012)
Recombinant expressionOrganism: Homo sapiens (human)

-
Supramolecule #3: Fab from IgG CR9114

SupramoleculeName: Fab from IgG CR9114 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 50 KDa

-
Supramolecule #4: Single-domain antibody SD84

SupramoleculeName: Single-domain antibody SD84 / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 25 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 210000
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 26000
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: EMAN2
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
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