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- EMDB-70111: Cryo-EM structure of Z1A11-GL Fab in complex with influenza virus... -

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Basic information

Entry
Database: EMDB / ID: EMD-70111
TitleCryo-EM structure of Z1A11-GL Fab in complex with influenza virus neuraminidase from A/California/07/2009 (H1N1)
Map data
Sample
  • Complex: Cryo-EM structure of Z1A11-GL Fab in complex with influenza virus neuraminidase from A/California/07/2009 (H1N1)
    • Protein or peptide: Neuraminidase
    • Protein or peptide: Z1A11-GL heavy chain
    • Protein or peptide: Z1A11-GL light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsNeuraminidase / Hydrolase / Antibody complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 (A/California/07/2009(H1N1))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsJo G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of broad protection against influenza virus by human antibodies targeting the neuraminidase active site via a recurring motif in CDR H3.
Authors: Gyunghee Jo / Seiya Yamayoshi / Krystal M Ma / Olivia Swanson / Jonathan L Torres / James A Ferguson / Monica L Fernández-Quintero / Jiachen Huang / Jeffrey Copps / Alesandra J Rodriguez / ...Authors: Gyunghee Jo / Seiya Yamayoshi / Krystal M Ma / Olivia Swanson / Jonathan L Torres / James A Ferguson / Monica L Fernández-Quintero / Jiachen Huang / Jeffrey Copps / Alesandra J Rodriguez / Jon M Steichen / Yoshihiro Kawaoka / Julianna Han / Andrew B Ward /
Abstract: Influenza viruses evolve rapidly, driving seasonal epidemics and posing global pandemic threats. While neuraminidase (NA) has emerged as a vaccine target, shared molecular features of NA antibody ...Influenza viruses evolve rapidly, driving seasonal epidemics and posing global pandemic threats. While neuraminidase (NA) has emerged as a vaccine target, shared molecular features of NA antibody responses are still not well understood. Here, we describe cryo-electron microscopy structures of the broadly protective human antibody DA03E17, which was previously identified from an H1N1-infected donor, in complex with NA from A/H1N1, A/H3N2, and B/Victoria-lineage viruses. DA03E17 targets the highly conserved NA active site using its long CDR H3, which features a DR (Asp-Arg) motif that engages catalytic residues and mimics sialic acid interactions. We further demonstrate that this motif is conserved among several NA active site-targeting antibodies, indicating a common receptor mimicry strategy. We also identified BCR sequences containing this DR motif across all donors in a healthy human repertoire database, suggesting that such precursors may be relatively common and have vaccine targeting potential. Our findings reveal shared molecular features in NA active site-targeting antibodies that can be harnessed to design broad, immune-focused influenza vaccines.
History
DepositionApr 8, 2025-
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_70111.png

Downloads & links

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Map

FileDownload / File: emd_70111.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 371.2 Å		0.73 Å/pix.
x 512 pix.
= 371.2 Å		0.73 Å/pix.
x 512 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.14603485 - 0.33614284
Average (Standard dev.)0.00008625375 (±0.0072187483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 371.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_70111_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70111_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Z1A11-GL Fab in complex with influenza virus...

EntireName: Cryo-EM structure of Z1A11-GL Fab in complex with influenza virus neuraminidase from A/California/07/2009 (H1N1)
Components
  • Complex: Cryo-EM structure of Z1A11-GL Fab in complex with influenza virus neuraminidase from A/California/07/2009 (H1N1)
    • Protein or peptide: Neuraminidase
    • Protein or peptide: Z1A11-GL heavy chain
    • Protein or peptide: Z1A11-GL light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Cryo-EM structure of Z1A11-GL Fab in complex with influenza virus...

SupramoleculeName: Cryo-EM structure of Z1A11-GL Fab in complex with influenza virus neuraminidase from A/California/07/2009 (H1N1)
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 (A/California/07/2009(H1N1))
Molecular weightTheoretical: 52.806184 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYSMQLASCV TLTLVLLVNS QHHHHHHGSA WSHPQFEKGG SSSDYSDLQR VKQELLEEVK KELQKVKEEI IEAFVQELRK RGSLVPRGS GGVKLAGNSS LCPVSGWAPL SKDNSVRIGS KGDVFVIREP FISCSPLECR TFFLTQGALL NDKHSNGTIK D RSPYRTLM ...String:
MYSMQLASCV TLTLVLLVNS QHHHHHHGSA WSHPQFEKGG SSSDYSDLQR VKQELLEEVK KELQKVKEEI IEAFVQELRK RGSLVPRGS GGVKLAGNSS LCPVSGWAPL SKDNSVRIGS KGDVFVIREP FISCSPLECR TFFLTQGALL NDKHSNGTIK D RSPYRTLM SVPIGSVPSP YNARFESIAW SASACHDGIN WLTIGITGPD NGAVAILKYN GIITDTIKSW RNNILRTQES EC ACVNGSC FTVMTDGPSN GQASYKIFRI EKGKIVKSVE MNAPNYHYEE CSCYPDSSEI TCVCRDNWHG SNRPWVSFNQ NLE YQIGYI CSGIFGDNPR PNDKTGSCGP VSSNGANGVK GFSFKYGNGV WIGRTKSISS RNGFEMIWDP NGWTGTDNNF SIKQ DIVGI NEWSGYSGSF VMHPELTGLD CIVPCFWVEL IRGRPKENTI WTSGSSISFC GVNSDTVGWS WPDGAELPFT IDK

UniProtKB: Neuraminidase

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Macromolecule #2: Z1A11-GL heavy chain

MacromoleculeName: Z1A11-GL heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.024521 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGASVKV SCKASGYTFT SYYMHWVRQA PGQGLEWMGI INPSGGSTSY AQKFQGRVTM TRDTSTSTVY MELSSLRSE DTAVYYCARN SYYYDTDRPY YNGMDVWGQG TTVTVSS

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Macromolecule #3: Z1A11-GL light chain

MacromoleculeName: Z1A11-GL light chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.228683 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL HSNGYNYLDW YLQKPGQSPQ LLIYLGSNRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQAVQT PRTFGQGTRL 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: 9 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration0.4 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 2119 / Average exposure time: 3.06 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / Details: cryoSPARC - ab initio
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 134231
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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