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- EMDB-40046: CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) ... -

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Basic information

Entry
Database: EMDB / ID: EMD-40046
TitleCryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) hemagglutinin bound to GS10-X6-BE4 Fab
Map data
Sample
  • Complex: CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) hemagglutinin bound to GS10-X6-BE4 Fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: GS10-X6-BE4 Fab Heavy chain
    • Protein or peptide: GS10-X6-BE4 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNIAID / hemagglutinin stalk binding antibody / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: Structure / Year: 2024
Title: Structural basis for the broad antigenicity of the computationally optimized influenza hemagglutinin X6.
Authors: Kaito A Nagashima / John V Dzimianski / Meng Yang / Jan Abendroth / Giuseppe A Sautto / Ted M Ross / Rebecca M DuBois / Thomas E Edwards / Jarrod J Mousa /
Abstract: Influenza causes significant morbidity and mortality. As an alternative approach to current seasonal vaccines, the computationally optimized broadly reactive antigen (COBRA) platform has been ...Influenza causes significant morbidity and mortality. As an alternative approach to current seasonal vaccines, the computationally optimized broadly reactive antigen (COBRA) platform has been previously applied to hemagglutinin (HA). This approach integrates wild-type HA sequences into a single immunogen to expand the breadth of accessible antibody epitopes. Adding to previous studies of H1, H3, and H5 COBRA HAs, we define the structural features of another H1 subtype COBRA, X6, that incorporates HA sequences from before and after the 2009 H1N1 influenza pandemic. We determined structures of this antigen alone and in complex with COBRA-specific as well as broadly reactive and functional antibodies, analyzing its antigenicity. We found that X6 possesses features representing both historic and recent H1 HA strains, enabling binding to both head- and stem-reactive antibodies. Overall, these data confirm the integrity of broadly reactive antibody epitopes of X6 and contribute to design efforts for a next-generation vaccine.
History
DepositionMar 10, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40046.png

Downloads & links

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Map

FileDownload / File: emd_40046.map.gz / Format: CCP4 / Size: 662.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 558 pix.
= 376.65 Å		0.68 Å/pix.
x 558 pix.
= 376.65 Å		0.68 Å/pix.
x 558 pix.
= 376.65 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0632
Minimum - Maximum-0.30630875 - 0.49356607
Average (Standard dev.)-0.0000043298346 (±0.011300368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions558558558
Spacing558558558
CellA=B=C: 376.65 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_40046_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40046_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) ...

EntireName: CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) hemagglutinin bound to GS10-X6-BE4 Fab
Components
  • Complex: CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) hemagglutinin bound to GS10-X6-BE4 Fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: GS10-X6-BE4 Fab Heavy chain
    • Protein or peptide: GS10-X6-BE4 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) ...

SupramoleculeName: CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) hemagglutinin bound to GS10-X6-BE4 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 221 KDa

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: 1/Melbourne/1/1946(H1N1)
Molecular weightTheoretical: 53.994246 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCLLKGIAPL QLGNCSVAGW ILGNPECELL ISKESWSYIV ETPNPENGT CYPGYFADYE ELREQLSSVS SFERFEIFPK ESSWPNHTVT GVSASCSHNG KSSFYRNLLW LTGKNGLYPN L SKSYANNK ...String:
DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCLLKGIAPL QLGNCSVAGW ILGNPECELL ISKESWSYIV ETPNPENGT CYPGYFADYE ELREQLSSVS SFERFEIFPK ESSWPNHTVT GVSASCSHNG KSSFYRNLLW LTGKNGLYPN L SKSYANNK EKEVLVLWGV HHPPNIGDQR ALYHTENAYV SVVSSHYSRK FTPEIAKRPK VRDQEGRINY YWTLLEPGDT II FEANGNL IAPRYAFALS RGFGSGIITS NAPMDECDAK CQTPQGAINS SLPFQNVHPV TIGECPKYVR SAKLRMVTGL RNI PSIAGF IEGGWTGMVD GWYGYHHQNE QGSGYAADQK STQNAINGIT NKVNSVIEKM NTQFTAVGKE FNKLERRMEN LNKK VDDGF LDIWTYNAEL LVLLENERTL DFHDSNVKNL YEKVKSQLKN NAKEIGNGCF EFYHKCNNEC MESVKNGTYD YPKYS

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Macromolecule #2: GS10-X6-BE4 Fab Heavy chain

MacromoleculeName: GS10-X6-BE4 Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.154263 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVLGLKWVFF VVLYQGVHCE VQLVESGGGL VQPKGSLKLS CATSGFTFNT FDMHWVRQAP GKDLEWVARI RTKGNSYATY YAASVKDRI TISRDDSQSM LYLEMNSLRS EDTAMYYCVR EGGHYYGYYF DFWGQGTTLT VSS

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Macromolecule #3: GS10-X6-BE4 Fab light chain

MacromoleculeName: GS10-X6-BE4 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.949619 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSSAQFLGLL LLCFQGTRCE IQMTQTTSSL SASLGDRVTI SCRASQDIYN YLNWYQQQPD GAVKLLIYYT SKLHSGVPSR FSGSGSGTD YSLTITNLEQ EDIATYFCQQ GYTLPYTFGG GTKLEIK

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationName
150.0 mMsodium chloride
25.0 mMTris/HCl
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: LACEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7031 / Average exposure time: 2.4 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

8dis

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 100708
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8dis


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8ghk:
CryoEM structure of Influenza A virus A/Melbourner/1/1946 (H1N1) hemagglutinin bound to GS10-X6-BE4 Fab

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