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- EMDB-48102: NCS.1.1 Fab in complex with the sNAp of A/California/04/2009 (CA0... -

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Basic information

Entry
Database: EMDB / ID: EMD-48102
TitleNCS.1.1 Fab in complex with the sNAp of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]
Map dataSharpened map
Sample
  • Complex: NCS.1.1 Fab in complex with the sNAp of A/California/04/2009 (CA09, H1N1) -- 4 Fabs
    • Protein or peptide: Neuraminidase
    • Protein or peptide: NCS.1.1 Heavy Chain
    • Protein or peptide: NCS.1.1 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsNeuraminidase / NCS.1.1 / Tetramer / Antibody / Fab / N1 / H1N5 / CA09 / VIRAL PROTEIN
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsBorst AJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural convergence and water-mediated substrate mimicry enable broad neuraminidase inhibition by human antibodies.
Authors: Julia Lederhofer / Andrew J Borst / Lam Nguyen / Rebecca A Gillespie / Connor J Williams / Emma L Walker / Julie E Raab / Christina Yap / Daniel Ellis / Adrian Creanga / Hyon-Xhi Tan / Thi H ...Authors: Julia Lederhofer / Andrew J Borst / Lam Nguyen / Rebecca A Gillespie / Connor J Williams / Emma L Walker / Julie E Raab / Christina Yap / Daniel Ellis / Adrian Creanga / Hyon-Xhi Tan / Thi H T Do / Michelle Ravichandran / Adrian B McDermott / Valerie Le Sage / Sarah F Andrews / Barney S Graham / Adam K Wheatley / Douglas S Reed / Neil P King / Masaru Kanekiyo /
Abstract: Influenza has been responsible for multiple global pandemics and seasonal epidemics and claimed millions of lives. The imminent threat of a panzootic outbreak of avian influenza H5N1 virus ...Influenza has been responsible for multiple global pandemics and seasonal epidemics and claimed millions of lives. The imminent threat of a panzootic outbreak of avian influenza H5N1 virus underscores the urgent need for pandemic preparedness and effective countermeasures, including monoclonal antibodies (mAbs). Here, we characterize human mAbs that target the highly conserved catalytic site of viral neuraminidase (NA), termed NCS mAbs, and the molecular basis of their broad specificity. Cross-reactive NA-specific B cells were isolated by using stabilized NA probes of non-circulating subtypes. We found that NCS mAbs recognized multiple NAs of influenza A as well as influenza B NAs and conferred prophylactic protections in mice against H1N1, H5N1, and influenza B viruses. Cryo-electron microscopy structures of two NCS mAbs revealed that they rely on structural mimicry of sialic acid, the substrate of NA, by coordinating not only amino acid side chains but also water molecules, enabling inhibition of NA activity across multiple influenza A and B viruses, including avian influenza clade 2.3.4.4b H5N1 viruses. Our results provide a molecular basis for the broad reactivity and inhibitory activity of NCS mAbs targeting the catalytic site of NA through substrate mimicry.
History
DepositionNov 27, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48102.png

Downloads & links

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Map

FileDownload / File: emd_48102.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 460 pix.
= 407.1 Å		0.89 Å/pix.
x 460 pix.
= 407.1 Å		0.89 Å/pix.
x 460 pix.
= 407.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0656
Minimum - Maximum-0.4460062 - 0.7034595
Average (Standard dev.)-0.000022895392 (±0.01450519)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 407.1 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhanced map

Fileemd_48102_additional_1.map
AnnotationDeepEMhanced map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_48102_additional_2.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half A

Fileemd_48102_half_map_1.map
AnnotationHalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_48102_half_map_2.map
AnnotationHalf 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 : NCS.1.1 Fab in complex with the sNAp of A/California/04/2009 (CA0...

EntireName: NCS.1.1 Fab in complex with the sNAp of A/California/04/2009 (CA09, H1N1) -- 4 Fabs
Components
  • Complex: NCS.1.1 Fab in complex with the sNAp of A/California/04/2009 (CA09, H1N1) -- 4 Fabs
    • Protein or peptide: Neuraminidase
    • Protein or peptide: NCS.1.1 Heavy Chain
    • Protein or peptide: NCS.1.1 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: NCS.1.1 Fab in complex with the sNAp of A/California/04/2009 (CA0...

SupramoleculeName: NCS.1.1 Fab in complex with the sNAp of A/California/04/2009 (CA09, H1N1) -- 4 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 49.139934 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHSSSD YSDLQRVKQE LLEEVKKELQ KVKEEIIEAF VQELRKRGSL VPRGSGGVKL AGNSSLCPVS GWAPLSKDNS VRIGSKGDV FVIREPFISC SPLECRTFFL TQGALLNDKH SNGTIKDRSP YRTLMSVPIG SVPSPYNARF ESIAWSASAC H DGINWLTI ...String:
HHHHHHSSSD YSDLQRVKQE LLEEVKKELQ KVKEEIIEAF VQELRKRGSL VPRGSGGVKL AGNSSLCPVS GWAPLSKDNS VRIGSKGDV FVIREPFISC SPLECRTFFL TQGALLNDKH SNGTIKDRSP YRTLMSVPIG SVPSPYNARF ESIAWSASAC H DGINWLTI GITGPDNGAV AILKYNGIIT DTIKSWRNNI LRTQESECAC VNGSCFTVMT DGPSNGQASY KIFRIEKGKI VK SVEMNAP NYHYEECSCY PDSSEITCVC RDNWHGSNRP WVSFNQNLEY QIGYICSGIF GDNPRPNDKT GSCGPVSSNG ANG VKGFSF KYGNGVWIGR TKSISSRNGF EMIWDPNGWT GTDNNFSIKQ DIVGINEWSG YSGSFVMHPE LTGLDCIVPC FWVE LIRGR PKENTIWTSG SSISFCGVNS DTTGWSWPDG AELPFTIDK

UniProtKB: Neuraminidase

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Macromolecule #2: NCS.1.1 Heavy Chain

MacromoleculeName: NCS.1.1 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.012506 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPR LVKPSETLSL TCSVSGESIS SGGYYWTWIR QHPGKGLEWI GNIFDTGSTD YSPSLKTRLT ISIDTSKNQF YLRLNSATA ADTAVYYCAR VGFSLETDRP YYLGLDVWGQ GTTVTVSS

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Macromolecule #3: NCS.1.1 Light Chain

MacromoleculeName: NCS.1.1 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.252719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL HSNGYTYLDW YLQKPGQSPQ LLISFTSNRA SGVPDRFSGS GSGTYFTLKI SRVEAEDVG VYYCMQAVQT PWTFGQGTKV EIK

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 918 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 382836
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ejf:
NCS.1.1 Fab in complex with the sNAp of A/California/04/2009 (CA09, H1N1) -- 4 Fabs [C4 Reconstruction]

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