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- EMDB-39605: Neuraminidase of A/Red knot/Delaware Bay/310/2016 H10N4 in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-39605
TitleNeuraminidase of A/Red knot/Delaware Bay/310/2016 H10N4 in complex with CAV-F6 Fab
Map data
Sample
  • Complex: Neuraminidase of A/Red knot/Delaware Bay/310/2016 H10N4 in complex with CAV-F6 Fab
    • Protein or peptide: Neuraminidase
    • Protein or peptide: CAV-F6 heavy chain
    • Protein or peptide: CAV-F6 kappa chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
Keywordsinfluenza virus / neuraminidase / antibody / 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
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus (A/red knot/Delaware Bay/310/2016(H10N4)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsWang X / Ge J / Li X
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Neuraminidase of A/Red knot/Delaware Bay/310/2016 H10N4 in complex with CAV-F6 Fab
Authors: Wang X / Ge J / Li X
History
DepositionMar 28, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39605.png

Downloads & links

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Map

FileDownload / File: emd_39605.map.gz / Format: CCP4 / Size: 115.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 312 pix.
= 293.28 Å		0.94 Å/pix.
x 312 pix.
= 293.28 Å		0.94 Å/pix.
x 312 pix.
= 293.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.269
Minimum - Maximum-1.2586316 - 2.319107
Average (Standard dev.)-0.00064017536 (±0.07482217)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 293.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39605_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39605_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Neuraminidase of A/Red knot/Delaware Bay/310/2016 H10N4 in comple...

EntireName: Neuraminidase of A/Red knot/Delaware Bay/310/2016 H10N4 in complex with CAV-F6 Fab
Components
  • Complex: Neuraminidase of A/Red knot/Delaware Bay/310/2016 H10N4 in complex with CAV-F6 Fab
    • Protein or peptide: Neuraminidase
    • Protein or peptide: CAV-F6 heavy chain
    • Protein or peptide: CAV-F6 kappa chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Neuraminidase of A/Red knot/Delaware Bay/310/2016 H10N4 in comple...

SupramoleculeName: Neuraminidase of A/Red knot/Delaware Bay/310/2016 H10N4 in complex with CAV-F6 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus (A/red knot/Delaware Bay/310/2016(H10N4))

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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/red knot/Delaware Bay/310/2016(H10N4))
Molecular weightTheoretical: 42.809805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VHYSSGRDLC PIRGWAPLSK DNGIRIGSRG EVFVIREPFI SCSISECRTF FLTQGALLND KHSNGTVKDR SPFRTLMSCP IGVAPSPSN SRFESVAWSA TACSDGPGWL TLGITGPDST AVAVLKYNGI ITDTLKSWKG NIMRTQESEC VCQDEFCYTL V TDGPSDAQ ...String:
VHYSSGRDLC PIRGWAPLSK DNGIRIGSRG EVFVIREPFI SCSISECRTF FLTQGALLND KHSNGTVKDR SPFRTLMSCP IGVAPSPSN SRFESVAWSA TACSDGPGWL TLGITGPDST AVAVLKYNGI ITDTLKSWKG NIMRTQESEC VCQDEFCYTL V TDGPSDAQ AFYKILKIRK GKIVSMKDVD ATGFHFEECS CYPSGTEIEC VCRDNWRGSN RPWIRFNSDL DYQIGYVCSG IF GDNPRPV DGTGSCNGPV NNGKGRYGVK GFSFRYGDGV WIGRTKSLES RSGFEMVWDA NGWVSTDKDS NGVQDIIDND NWS GYSGSF SIRGETTGKN CTVPCFWVEM IRGQPKEKTI WTSGSSIAFC GVNSDTTGWS WPDGALLPFD IDK

UniProtKB: Neuraminidase

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Macromolecule #2: CAV-F6 heavy chain

MacromoleculeName: CAV-F6 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.569127 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVQPGGSLRL SCAASGFSFT TYEMNWVRQA PGKGLEWVSH ISSRGLVIYY ADSVKGRFTM SRDTAKNSLY LQMDSLTVA DTAVYYCARH YFDRDWGYSG MDLWGQGTTV TVSS

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Macromolecule #3: CAV-F6 kappa chain

MacromoleculeName: CAV-F6 kappa chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.642924 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVVLTQSPGT LSLSPGERAT LSCRASQSLG TNYLAWYQHK PGQSPRLLID GASTRAIGIP DRFSASGSGT DFTLTVSRLE PEDFAVYYC QHYGNPYTFG QGTKLEIK

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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: 4 / 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: 4 / 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

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE / Details: alphafold 2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17312
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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