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- EMDB-60391: Cryo-EM structure of the N2-4N2C402 complex at a resolution of 1.... -

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Basic information

Entry
Database: EMDB / ID: EMD-60391
TitleCryo-EM structure of the N2-4N2C402 complex at a resolution of 1.9 angstrom
Map dataCryo-EM map of the N2-4N2C402 complex
Sample
  • Complex: A complex of N2 with 4N2C402-Fab
    • Protein or peptide: 4N2C402_Fab_H
    • Protein or peptide: 4N2C402_Fab_L
    • Protein or peptide: Neuraminidase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: water
Keywordsviral enzyme / antibody / complex / inhibitor / VIRAL PROTEIN/IMMUNE SYSTEM / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsChu BX / Wang X / Yang Q / Wu XD / Zhang ZL
Funding support China, 1 items
OrganizationGrant numberCountry
Other private China
CitationJournal: Cell Host Microbe / Year: 2024
Title: Profiling influenza neuraminidase pre-existing humoral immunity in humans
Authors: Wang X / Yang Q / Chu BX / Wu XD / Zhang ZL
History
DepositionJun 3, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60391.png

Downloads & links

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Map

FileDownload / File: emd_60391.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the N2-4N2C402 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 350 pix.
= 322. Å		0.92 Å/pix.
x 350 pix.
= 322. Å		0.92 Å/pix.
x 350 pix.
= 322. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.4767908 - 2.7775452
Average (Standard dev.)0.000111670146 (±0.04575454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 322.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfmap A

Fileemd_60391_half_map_1.map
Annotationhalfmap_A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap B

Fileemd_60391_half_map_2.map
Annotationhalfmap_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 : A complex of N2 with 4N2C402-Fab

EntireName: A complex of N2 with 4N2C402-Fab
Components
  • Complex: A complex of N2 with 4N2C402-Fab
    • Protein or peptide: 4N2C402_Fab_H
    • Protein or peptide: 4N2C402_Fab_L
    • Protein or peptide: Neuraminidase
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: A complex of N2 with 4N2C402-Fab

SupramoleculeName: A complex of N2 with 4N2C402-Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: 4N2C402_Fab_H

MacromoleculeName: 4N2C402_Fab_H / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.059547 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QGRLQESGGG VVQPRRSLTL SCAASGFTLE TYTMHWVRQT PGKGLEWVAV SSKDGNNVYY RDSVKGRFTV SRDNSKNTLF LQMNHLRAE DTALYYCARG SDPDYDKGWG AYRNTDRPSY DGLDVWGQGT TVTVSS

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Macromolecule #2: 4N2C402_Fab_L

MacromoleculeName: 4N2C402_Fab_L / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.490856 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPLF LSVTPGESAS ISCRSSQSLL HSNGYNYLDW YLQKPGQSPQ LLIYWGSNRA SGVSDRFSGR GSGTDFTLTI YNVEAEDVG VYYCMQALQT PPWTFGQGTK VDIK

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Macromolecule #3: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 43.361598 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ICPKPAEYRN WSKPQCGITG FAPFSKDNSI RLSAGGDIWV TREPYVSCDP DKCYQFALGQ GTTINNVHSN NTARDRTPHR TLLMNELGV PFHLGTKQVC IAWSSSSCHD GKAWLHVCIT GDDKNATASF IYNGRLVDSV VSWSKDILRT QESECVCING T CTVVMTDG ...String:
ICPKPAEYRN WSKPQCGITG FAPFSKDNSI RLSAGGDIWV TREPYVSCDP DKCYQFALGQ GTTINNVHSN NTARDRTPHR TLLMNELGV PFHLGTKQVC IAWSSSSCHD GKAWLHVCIT GDDKNATASF IYNGRLVDSV VSWSKDILRT QESECVCING T CTVVMTDG NATGKADTKI LFIEEGKIVH TSKLSGSAQH VEECSCYPRY PGVRCVCRDN WKGSNRPIVD INIKDHSIVS SY VCSGLVG DTPRKTDSSS SSHCLNPNNE KGGHGVKGWA FDDGNDVWMG RTINETSRLG YETFKVVEGW SNPKSKLQIN RQV IVDRGD RSGYSGIFSV EGKSCINRCF YVELIRGRKE ETEVLWTSNS IVVFCGTSGT YGTGSWPDGA DLNLMHI

UniProtKB: Neuraminidase

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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: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 789 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 663111
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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