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- EMDB-49462: N1 neuraminidase of influenza A/Vietnam/1203/2004 H5N1 in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-49462
TitleN1 neuraminidase of influenza A/Vietnam/1203/2004 H5N1 in complex with four FNI9 Fab molecules
Map dataSharpened map
Sample
  • Complex: N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1) in complex with FNI9 Fab
    • Complex: N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1)
      • Protein or peptide: Neuraminidase
    • Complex: FNI9 Fab
      • Protein or peptide: FNI9 Fab heavy chain
      • Protein or peptide: FNI9 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
Keywordsantibody / neuraminidase / N1 / H5N1 / influenza / neutralizing antibody / 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 / identical protein binding
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus (A/Viet Nam/1203/2004(H5N1)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsErrico JM / Dang HV / Snell G
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP22fk0108141 Japan
Japan Agency for Medical Research and Development (AMED)JP243fa627005 Japan
Japan Agency for Medical Research and Development (AMED)JP243fa727002 Japan
CitationJournal: To Be Published
Title: Potent efficacy of a NA-targeting antibody against a broad spectrum of H5N1 influenza viruses
Authors: Moriyama S / Di Iulio J / Zatta F / Hauser K / Asanuma H / Munoz HE / Errico JM / Adachi Y / Dang HV / Czudnochowski N / Sasaki E / Chen A / Chen Y / Kotaki R / Peter A / Vetti E / Onodera T ...Authors: Moriyama S / Di Iulio J / Zatta F / Hauser K / Asanuma H / Munoz HE / Errico JM / Adachi Y / Dang HV / Czudnochowski N / Sasaki E / Chen A / Chen Y / Kotaki R / Peter A / Vetti E / Onodera T / Maher MC / Rosen LE / Shirakura M / Snell G / Hasegawa H / Takahashi Y / Corti D / Pizzuto MS
History
DepositionFeb 26, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49462.png

Downloads & links

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Map

FileDownload / File: emd_49462.map.gz / Format: CCP4 / Size: 178 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.)
0.82 Å/pix.
x 360 pix.
= 294.804 Å		0.82 Å/pix.
x 360 pix.
= 294.804 Å		0.82 Å/pix.
x 360 pix.
= 294.804 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8189 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065
Minimum - Maximum-0.033889532 - 0.06178576
Average (Standard dev.)0.00003196628 (±0.0017884995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 294.80402 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 1

Fileemd_49462_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_49462_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 : N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1) in com...

EntireName: N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1) in complex with FNI9 Fab
Components
  • Complex: N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1) in complex with FNI9 Fab
    • Complex: N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1)
      • Protein or peptide: Neuraminidase
    • Complex: FNI9 Fab
      • Protein or peptide: FNI9 Fab heavy chain
      • Protein or peptide: FNI9 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1) in com...

SupramoleculeName: N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1) in complex with FNI9 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1)

SupramoleculeName: N1 neuraminidase from Influenza A/Vietnam/1203/2004 (H5N1)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus (A/Viet Nam/1203/2004(H5N1))

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Supramolecule #3: FNI9 Fab

SupramoleculeName: FNI9 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#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/Viet Nam/1203/2004(H5N1)) / Strain: A/Vietnam/1203/2004 H5N1
Molecular weightTheoretical: 51.769551 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: HHHHHHGSGL NDIFEAQKIE WHEGSIINET ADDIVYRLTV IIDDRYESLK NLITLRADRL EMIINDNVST ILASGLVPRG SGSVKLAGN SSLCPINGWA VYSKDNSIRI GSKGDVFVIR EPFISCSHLE CRTFFLTQGA LLNDKHSNGT VKDRSPHRTL M SCPVGEAP ...String:
HHHHHHGSGL NDIFEAQKIE WHEGSIINET ADDIVYRLTV IIDDRYESLK NLITLRADRL EMIINDNVST ILASGLVPRG SGSVKLAGN SSLCPINGWA VYSKDNSIRI GSKGDVFVIR EPFISCSHLE CRTFFLTQGA LLNDKHSNGT VKDRSPHRTL M SCPVGEAP SPYNSRFESV AWSASACHDG TSWLTIGISG PDNGAVAVLK YNGIITDTIK SWRNNILRTQ ESECACVNGS CF TVMTDGP SNGQASHKIF KMEKGKVVKS VELDAPNYHY EECSCYPNAG EITCVCRDNW HGSNRPWVSF NQNLEYQIGY ICS GVFGDN PRPNDGTGSC GPVSSNGAYG VKGFSFKYGN GVWIGRTKST NSRSGFEMIW DPNGWTETDS SFSVKQDIVA ITDW SGYSG SFVQHPELTG LDCIRPCFWV ELIRGRPKES TIWTSGSSIS FCGVNSDTVG WSWPDGAELP FTIDK

UniProtKB: Neuraminidase

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Macromolecule #2: FNI9 Fab heavy chain

MacromoleculeName: FNI9 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.850109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVHLVQSGAE VKEPGSSVTV SCKASGGSFN NQAISWVRQA PGQGLEWMGG IFPISGTPTS AQRFQGRVTF TADESTTTVY MDLSSLRSD DTAVYYCARA GSDYFNRDLG WENYYFASWG QGTLVTVSS

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Macromolecule #3: FNI9 Fab light chain

MacromoleculeName: FNI9 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.805045 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVMTQSPAT LSLSSGERAT LSCRASRSVS SNLAWYQQKP GQAPRLLIYD ASTRATGFSA RFAGSGSGTE FTLTISSLQS EDSAIYYCQ QYNNWPPWTF GQGTKVEIK

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / 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

Concentration3.0 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 166858
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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