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- EMDB-43008: Fab fragment of human mAb #58 in complex with computationally opt... -

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Basic information

Entry
Database: EMDB / ID: EMD-43008
TitleFab fragment of human mAb #58 in complex with computationally optimized broadly reactive H1 influenza hemagglutinin X6
Map data
Sample
  • Complex: Complex of COBRA HA X6 with #58 Fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: #58 heavy chain
    • Protein or peptide: #58 light chain
KeywordsComplex / antibody / hemagglutinin / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsNagashima KA / Mousa JJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00052 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
DepositionDec 4, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43008.png

Downloads & links

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Map

FileDownload / File: emd_43008.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.526 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.4137481 - 0.60217446
Average (Standard dev.)0.00014247451 (±0.017075507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 315.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_43008_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43008_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43008_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of COBRA HA X6 with #58 Fab

EntireName: Complex of COBRA HA X6 with #58 Fab
Components
  • Complex: Complex of COBRA HA X6 with #58 Fab
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: #58 heavy chain
    • Protein or peptide: #58 light chain

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Supramolecule #1: Complex of COBRA HA X6 with #58 Fab

SupramoleculeName: Complex of COBRA HA X6 with #58 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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
Molecular weightTheoretical: 62.494656 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 PSIQSR GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLE RRMEN LNKKVDDGFL DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNNECM ESVKN GTYD YPKYSEESKL NREKIDGVGT GYIPEAPRDG QAYVRKDGEW VLLSTFLGSG LNDIFEAQKI EWHEGHHHHH H

UniProtKB: Hemagglutinin

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Macromolecule #2: #58 heavy chain

MacromoleculeName: #58 heavy chain / type: protein_or_peptide / ID: 2
Details: Heavy chain Fab fragment variable region of human mAb #58
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.052598 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCNVSGGSIN SYYWSWIRQP PGKGLEWIGY VYHSGSTHYN PSLNSRVTIS VDTSKRQFSL KLRSVTAAD TAVYYCAREK SDFWTVDSFF YYMDVWGRGT TVTVSS

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Macromolecule #3: #58 light chain

MacromoleculeName: #58 light chain / type: protein_or_peptide / ID: 3
Details: Kappa chain Fab fragment variable region of human mAb #58
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.797213 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPAT LSLSPGERAT LSCRASQSVA TSLAWYQQKP GQPPRLLIYD ASHRATAIPA RFTGSGSGTD FTLTISSLEP EDFAVYYCQ QRTHWPPALT FGGGTKVEIK

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 57.22 e/Å2

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Image processing

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

8f38

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110051

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