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- EMDB-2140: EM map of influenza H2 hemagglutatin in complex with C05 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-2140
TitleEM map of influenza H2 hemagglutatin in complex with C05 Fab
Map dataNegative stain reconstruction of flu H2 HA in complex with C05 fab fragment
Sample
  • Sample: Influenza HA2 from A/Japan/305/1957 in complex with C5 Fab
  • Protein or peptide: Influenza A/Japan/305/1957 hemagglutinin
  • Protein or peptide: C05 antibody fab fragment
KeywordsInfluenza A / flu / hemagglutanin / HA neutralizing antibody / C5 fab / C05
Biological speciesInfluenza A virus (A/Japan/305/1957(H2N2)) / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 Å
AuthorsKhayat R / Lee JH / Ekiert DC / Wilson IA / Ward AB
CitationJournal: Nature / Year: 2012
Title: Cross-neutralization of influenza A viruses mediated by a single antibody loop.
Authors: Damian C Ekiert / Arun K Kashyap / John Steel / Adam Rubrum / Gira Bhabha / Reza Khayat / Jeong Hyun Lee / Michael A Dillon / Ryann E O'Neil / Aleksandr M Faynboym / Michael Horowitz / ...Authors: Damian C Ekiert / Arun K Kashyap / John Steel / Adam Rubrum / Gira Bhabha / Reza Khayat / Jeong Hyun Lee / Michael A Dillon / Ryann E O'Neil / Aleksandr M Faynboym / Michael Horowitz / Lawrence Horowitz / Andrew B Ward / Peter Palese / Richard Webby / Richard A Lerner / Ramesh R Bhatt / Ian A Wilson /
Abstract: Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that ...Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that can be targeted. Single protein loops can mediate extremely high-affinity binding, but it is unclear whether such a mechanism is available to antibodies. Here we report the isolation and characterization of an antibody called C05, which neutralizes strains from multiple subtypes of influenza A virus, including H1, H2 and H3. X-ray and electron microscopy structures show that C05 recognizes conserved elements of the receptor-binding site on the haemagglutinin surface glycoprotein. Recognition of the haemagglutinin receptor-binding site is dominated by a single heavy-chain complementarity-determining region 3 loop, with minor contacts from heavy-chain complementarity-determining region 1, and is sufficient to achieve nanomolar binding with a minimal footprint. Thus, binding predominantly with a single loop can allow antibodies to target small, conserved functional sites on otherwise hypervariable antigens.
History
DepositionJun 25, 2012-
Header (metadata) releaseJul 9, 2012-
Map releaseSep 19, 2012-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2140.png

Downloads & links

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Map

FileDownload / File: emd_2140.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain reconstruction of flu H2 HA in complex with C05 fab fragment
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 100 pix.
= 218. Å		2.18 Å/pix.
x 100 pix.
= 218. Å		2.18 Å/pix.
x 100 pix.
= 218. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.15 / Movie #1: 4.15
Minimum - Maximum-2.20667315 - 16.81837273
Average (Standard dev.)0.41255367 (±1.9614259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 218.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.182.182.18
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z218.000218.000218.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-2.20716.8180.413

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Supplemental data

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Sample components

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Entire : Influenza HA2 from A/Japan/305/1957 in complex with C5 Fab

EntireName: Influenza HA2 from A/Japan/305/1957 in complex with C5 Fab
Components
  • Sample: Influenza HA2 from A/Japan/305/1957 in complex with C5 Fab
  • Protein or peptide: Influenza A/Japan/305/1957 hemagglutinin
  • Protein or peptide: C05 antibody fab fragment

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Supramolecule #1000: Influenza HA2 from A/Japan/305/1957 in complex with C5 Fab

SupramoleculeName: Influenza HA2 from A/Japan/305/1957 in complex with C5 Fab
type: sample / ID: 1000 / Oligomeric state: One HA trimer binds to 3 fabs / Number unique components: 2

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Macromolecule #1: Influenza A/Japan/305/1957 hemagglutinin

MacromoleculeName: Influenza A/Japan/305/1957 hemagglutinin / type: protein_or_peptide / ID: 1 / Name.synonym: HA2 / Number of copies: 3 / Oligomeric state: Trimer / Recombinant expression: Yes
Source (natural)Organism: Influenza A virus (A/Japan/305/1957(H2N2)) / Strain: A/Japan/305/1957 / synonym: Flu
Recombinant expressionOrganism: unidentified baculovirus / Recombinant plasmid: pDCE198

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Macromolecule #2: C05 antibody fab fragment

MacromoleculeName: C05 antibody fab fragment / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: unidentified baculovirus / Recombinant plasmid: pFastBacDual

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 20mM HEPES pH 7.5, 50mM NaCl
StainingType: NEGATIVE / Details: Nano-W for 30 seconds
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 293 K / Max: 293 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism corrected at 100,000x
DetailsImages acquired from 0 to 55 degrees in 5 degree tilt increments.
DateFeb 14, 2012
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 0.109 µm / Number real images: 252 / Average electron dose: 16 e/Å2 / Details: Images recorded using CCD / Bits/pixel: 16
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 55
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected using an automated particle picking program.
CTF correctionDetails: Micrograph and each particle
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Sparx / Number images used: 31446

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