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- EMDB-9029: Hemagglutinin trimeric ectodomain (B/Massachusetts/02/2012) in co... -

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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 CR9114Fragment antigen-binding
    • 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

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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

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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

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Supplemental data

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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)

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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)

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Sample components

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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 CR9114Fragment antigen-binding
    • Complex: Single-domain antibody SD84

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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

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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)

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Particle selectionNumber selected: 210000
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: EMAN2
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
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
FSC plot (resolution estimation)

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