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- EMDB-28729: Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) inf... -

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Basic information

Entry
Database: EMDB / ID: EMD-28729
TitleStructure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
Map dataStructure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
Sample
  • Complex: Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
    • Protein or peptide: Heavy chain of influenza virus neuraminidase antibody 1F04
    • Protein or peptide: Light chain of influenza virus neuraminidase antibody 1F04
    • Protein or peptide: Neuraminidase
  • Ligand: alpha-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody / neuraminidase / influenza / Hydrolase-Immune System complex
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus / Homo sapiens (human) / Influenza A virus (A/Moscow/10/1999(H3N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMou Z / Lei R / Wu NC / Dai X
Funding support4 items
OrganizationGrant numberCountry
Other governmentR01 AI167910
Other governmentDP2 AT011966
Other privateMichelson Prizes for Human Immunology and Vaccine Research
Other privateSearle Scholars Program
CitationJournal: Immunity / Year: 2023
Title: Leveraging vaccination-induced protective antibodies to define conserved epitopes on influenza N2 neuraminidase.
Authors: Ruipeng Lei / Wooseob Kim / Huibin Lv / Zongjun Mou / Michael J Scherm / Aaron J Schmitz / Jackson S Turner / Timothy J C Tan / Yiquan Wang / Wenhao O Ouyang / Weiwen Liang / Joel Rivera- ...Authors: Ruipeng Lei / Wooseob Kim / Huibin Lv / Zongjun Mou / Michael J Scherm / Aaron J Schmitz / Jackson S Turner / Timothy J C Tan / Yiquan Wang / Wenhao O Ouyang / Weiwen Liang / Joel Rivera-Cardona / Chuyun Teo / Claire S Graham / Christopher B Brooke / Rachel M Presti / Chris K P Mok / Florian Krammer / Xinghong Dai / Ali H Ellebedy / Nicholas C Wu /
Abstract: There is growing appreciation for neuraminidase (NA) as an influenza vaccine target; however, its antigenicity remains poorly characterized. In this study, we isolated three broadly reactive N2 ...There is growing appreciation for neuraminidase (NA) as an influenza vaccine target; however, its antigenicity remains poorly characterized. In this study, we isolated three broadly reactive N2 antibodies from the plasmablasts of a single vaccinee, including one that cross-reacts with NAs from seasonal H3N2 strains spanning five decades. Although these three antibodies have diverse germline usages, they recognize similar epitopes that are distant from the NA active site and instead involve the highly conserved underside of NA head domain. We also showed that all three antibodies confer prophylactic and therapeutic protection in vivo, due to both Fc effector functions and NA inhibition through steric hindrance. Additionally, the contribution of Fc effector functions to protection in vivo inversely correlates with viral growth inhibition activity in vitro. Overall, our findings advance the understanding of NA antibody response and provide important insights into the development of a broadly protective influenza vaccine.
History
DepositionOct 31, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28729.png

Downloads & links

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Map

FileDownload / File: emd_28729.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-6.7002344 - 9.423080000000001
Average (Standard dev.)-0.0013193551 (±0.20190541)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_28729_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_28729_half_map_2.map
AnnotationHalf 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 : Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) inf...

EntireName: Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
Components
  • Complex: Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
    • Protein or peptide: Heavy chain of influenza virus neuraminidase antibody 1F04
    • Protein or peptide: Light chain of influenza virus neuraminidase antibody 1F04
    • Protein or peptide: Neuraminidase
  • Ligand: alpha-D-mannopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) inf...

SupramoleculeName: Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Structure of 1F04 Fab in complex with A/Moscow/10/1999 (H3N2) influenza virus neuraminidase
Source (natural)Organism: Influenza A virus

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Macromolecule #1: Heavy chain of influenza virus neuraminidase antibody 1F04

MacromoleculeName: Heavy chain of influenza virus neuraminidase antibody 1F04
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.984465 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVLPGRSLRL SCVASGFDFS SFEMNWVRQA PGTGLEWLSY ISGNGDTIYY AESVKGRFTI SRDNAKNSLY LQMNGLRAE DTATYYCARQ RSVYSTSRSN WSVFLDDWGQ GTLVTVS

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Macromolecule #2: Light chain of influenza virus neuraminidase antibody 1F04

MacromoleculeName: Light chain of influenza virus neuraminidase antibody 1F04
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.8201 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGESAT LSCRASQSLA PNYLAWFQQQ PGQAPRLLIY GASSRAAGIP DRFSGSGSGT DFTLTITRLE PEDFAVYYC QQYGGSPPYT FGQGTKVEIK R

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Macromolecule #3: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus (A/Moscow/10/1999(H3N2))
Molecular weightTheoretical: 42.767715 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: AEYRNWSKPQ CNITGFAPFS KDNSIRLSAG GDIWVTREPY VSCDPDKCYQ FALGQGTTLN NGHSNDTVHD RTPYRTLLMN ELGVPFHLG TKQVCIAWSS SSCHDGKAWL HVCVTGDDEN ATASFIYNGR LVDSIGSWSK KILRTQESEC VCINGTCTVV M TDGSASGK ...String:
AEYRNWSKPQ CNITGFAPFS KDNSIRLSAG GDIWVTREPY VSCDPDKCYQ FALGQGTTLN NGHSNDTVHD RTPYRTLLMN ELGVPFHLG TKQVCIAWSS SSCHDGKAWL HVCVTGDDEN ATASFIYNGR LVDSIGSWSK KILRTQESEC VCINGTCTVV M TDGSASGK ADTKILFIEE GKIVHTSPLS GSAQHVEECS CYPRYPGVRC VCRDNWKGSN RPIVDINVKD YSIVSSYVCS GL VGDTPRK NDSSSSSHCL DPNNEEGGHG VKGWAFDDGN DVWMGRTISE KLRSGYETFK VIEGWSKPNS KLQINRQVIV DRG NRSGYS GIFSVEGKSC INRCFYVELI RGRKQETEVL WTSNSIVVFC GTSGTYGTGS WPDGADINLM PI

UniProtKB: Neuraminidase

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Macromolecule #5: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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: 3 / 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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 480812
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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