8YVN | pdb_00008yvn

Neuraminidase of A/Switzerland/9715293/2013 H3N2 in complex with CAV-F6 Fab

PDB DOI: https://doi.org/10.2210/pdb8YVN/pdb
EM Map EMD-39609: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Influenza A virus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-03-28 Released: 2025-07-02
Deposition Author(s): Wang, X., Ge, J., Li, X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Neuraminidase of A/Switzerland/9715293/2013 H3N2 in complex with CAV-F6 Fab

Wang, X., Ge, J., Li, X.

To be published.

Macromolecule Content

Total Structure Weight: 284.3 kDa
Atom Count: 19,880
Modeled Residue Count: 2,468
Deposited Residue Count: 2,468
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A, B, C, D	387	Influenza A virus	Mutation(s): 0 Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for A0A0N7G9M6 (Influenza A virus) Explore A0A0N7G9M6 Go to UniProtKB: A0A0N7G9M6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0N7G9M6
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CAV-F6 heavy chain	E, F, G, H	123	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CAV-F6 kappa chain	I, J, K, L	107	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, Q, U, Y	3		N-Glycosylation	Interactions Focus chain M Focus chain Q Focus chain U Focus chain Y Interactions & Density Focus chain M Focus chain Q Focus chain U Focus chain Y
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], N, O, R, S, AA [auth a], N, O, R, S, V, W, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain N Focus chain O Focus chain R Focus chain S Focus chain V Focus chain W Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain N Focus chain O Focus chain R Focus chain S Focus chain V Focus chain W Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], P, T, X	7		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain P Focus chain T Focus chain X Interactions & Density Focus chain BA [auth b] Focus chain P Focus chain T Focus chain X
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain LA [auth D] SDF format, chain MA [auth D] SDF format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain MA [auth D] MOL2 format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain MA [auth D] mmCIF format, chain CA [auth A]	CA [auth A] DA [auth A] FA [auth B] GA [auth B] IA [auth C] CA [auth A], DA [auth A], FA [auth B], GA [auth B], IA [auth C], JA [auth C], LA [auth D], MA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain LA [auth D] Focus chain MA [auth D] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain LA [auth D] Focus chain MA [auth D]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain HA [auth B] SDF format, chain KA [auth C] SDF format, chain NA [auth D] MOL2 format, chain EA [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain NA [auth D] mmCIF format, chain EA [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain NA [auth D]	EA [auth A], HA [auth B], KA [auth C], NA [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain HA [auth B] Focus chain KA [auth C] Focus chain NA [auth D] Interactions & Density Focus chain EA [auth A] Focus chain HA [auth B] Focus chain KA [auth C] Focus chain NA [auth D]