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- EMDB-42149: S1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004 -

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Basic information

Entry
Database: EMDB / ID: EMD-42149
TitleS1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004
Map dataCryoEM map of S1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004
Sample
  • Complex: Complex of two S1V2-72 Fabs with postfusion HA2
    • Protein or peptide: S1V2-72 heavy chain
    • Protein or peptide: S1V2-72 light chain
    • Protein or peptide: Hemagglutinin
Keywordsimmunoglobulin / complex / hemagglutinin / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / endocytosis involved in viral entry into 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 B / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza B virus (B/Malaysia/2506/2004) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.98 Å
AuthorsFinney J / Kong S / Walsh Jr RM / Harrison SC / Kelsoe G
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI155804 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Protective human antibodies against a conserved epitope in pre- and postfusion influenza hemagglutinin.
Authors: Joel Finney / Annie Park Moseman / Susan Kong / Akiko Watanabe / Shengli Song / Richard M Walsh / Masayuki Kuraoka / Ryutaro Kotaki / E Ashley Moseman / Kevin R McCarthy / Dongmei Liao / ...Authors: Joel Finney / Annie Park Moseman / Susan Kong / Akiko Watanabe / Shengli Song / Richard M Walsh / Masayuki Kuraoka / Ryutaro Kotaki / E Ashley Moseman / Kevin R McCarthy / Dongmei Liao / Xiaoe Liang / Xiaoyan Nie / Olivia Lavidor / Richard Abbott / Stephen C Harrison / Garnett Kelsoe /
Abstract: Phylogenetically and antigenically distinct influenza A and B viruses (IAV and IBV) circulate in human populations, causing widespread morbidity. Antibodies (Abs) that bind epitopes conserved in both ...Phylogenetically and antigenically distinct influenza A and B viruses (IAV and IBV) circulate in human populations, causing widespread morbidity. Antibodies (Abs) that bind epitopes conserved in both IAV and IBV hemagglutinins (HAs) could protect against disease by diverse virus subtypes. Only one reported HA Ab, isolated from a combinatorial display library, protects against both IAV and IBV. Thus, there has been so far no information on the likelihood of finding naturally occurring human Abs that bind HAs of diverse IAV subtypes and IBV lineages. We have now recovered from several unrelated human donors five clonal Abs that bind a conserved epitope preferentially exposed in the postfusion conformation of IAV and IVB HA2. These Abs lack neutralizing activity in vitro but in mice provide strong, IgG subtype-dependent protection against lethal IAV and IBV infections. Strategies to elicit similar Abs routinely might contribute to more effective influenza vaccines.
History
DepositionSep 28, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42149.png

Downloads & links

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Map

FileDownload / File: emd_42149.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of S1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004
Voxel sizeX=Y=Z: 1.54688 Å
Density
Contour LevelBy AUTHOR: 0.679
Minimum - Maximum-1.9866364 - 3.325243
Average (Standard dev.)-0.0010721007 (±0.07520967)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: cryoEM Half-map A

Fileemd_42149_half_map_1.map
AnnotationcryoEM Half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryoEM Half-map B

Fileemd_42149_half_map_2.map
AnnotationcryoEM Half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of two S1V2-72 Fabs with postfusion HA2

EntireName: Complex of two S1V2-72 Fabs with postfusion HA2
Components
  • Complex: Complex of two S1V2-72 Fabs with postfusion HA2
    • Protein or peptide: S1V2-72 heavy chain
    • Protein or peptide: S1V2-72 light chain
    • Protein or peptide: Hemagglutinin

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Supramolecule #1: Complex of two S1V2-72 Fabs with postfusion HA2

SupramoleculeName: Complex of two S1V2-72 Fabs with postfusion HA2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1
Details: Fab fragment generated by proteolytic cleavage of S1V2-72 IgG
Source (natural)Organism: Influenza B virus (B/Malaysia/2506/2004)

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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 B virus (B/Malaysia/2506/2004)
Molecular weightTheoretical: 17.16916 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GYTSHGAHGV AVAADLKSTQ EAINKITKNL NSLSELEVKN LQRLSGAMDE IHNEILELDE KVDDLRADTI SSQIELAVLL SNEGIINSE DEHLLALERK LKKMLGPSAV DIGNGCFETK HKCNQTCLDR IAAGTFNAGE FSLPTFDSLN ITAASLNDDG

UniProtKB: Hemagglutinin

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Macromolecule #2: S1V2-72 heavy chain

MacromoleculeName: S1V2-72 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.135121 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE LKKPGASVKV SCKASGYTFT GNYIHWMRQV PGQGLEWMGW INPRTGDTHH AQKFQGRVDM TRDTSINTAY LELTRLESD DTALYYCARC VFATSQFDPW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
QVQLVQSGAE LKKPGASVKV SCKASGYTFT GNYIHWMRQV PGQGLEWMGW INPRTGDTHH AQKFQGRVDM TRDTSINTAY LELTRLESD DTALYYCARC VFATSQFDPW GQGTLVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVE PKSCDK

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Macromolecule #3: S1V2-72 light chain

MacromoleculeName: S1V2-72 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.755045 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPASV SGSPGQSITI SCTGTNSDIG SHNLVSWYQQ HPGKAPKVMI YDDSKRPSGV SNRFSGSKSG STASLTISGL QSEDEADYY CCSYAGSSNW VFGGGTKLTL LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSALTQPASV SGSPGQSITI SCTGTNSDIG SHNLVSWYQQ HPGKAPKVMI YDDSKRPSGV SNRFSGSKSG STASLTISGL QSEDEADYY CCSYAGSSNW VFGGGTKLTL LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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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
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 76.12 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 59527
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8udg:
S1V2-72 Fab bound to EHA2 from influenza B/Malaysia/2506/2004

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