8YVM | pdb_00008yvm

Neuraminidase of A/Switzerland/9715293/2013 H3N2 in complex with CAV-F34 Fab

PDB DOI: https://doi.org/10.2210/pdb8YVM/pdb
EM Map EMD-39608: 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: 3.02 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-F34 Fab

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

To be published.

Macromolecule Content

Total Structure Weight: 209.06 kDa
Atom Count: 14,579
Modeled Residue Count: 1,778
Deposited Residue Count: 1,778
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-F34 kappa chain	E	107	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-F34 heavy chain	F	123	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	G, K, O, S	3		N-Glycosylation	Interactions Focus chain G Focus chain K Focus chain O Focus chain S Interactions & Density Focus chain G Focus chain K Focus chain O Focus chain S
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	H, I, L, M, P H, I, L, M, P, Q, T, U	2		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain L Focus chain M Focus chain P Focus chain Q Focus chain T Focus chain U Interactions & Density Focus chain H Focus chain I Focus chain L Focus chain M Focus chain P Focus chain Q Focus chain T Focus chain U
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)]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	J, N, R, V	8		N-Glycosylation	Interactions Focus chain J Focus chain N Focus chain R Focus chain V Interactions & Density Focus chain J Focus chain N Focus chain R Focus chain V
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

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 Z [auth B] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain DA [auth C] SDF format, chain CA [auth C] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain AA [auth B]	AA [auth B] CA [auth C] DA [auth C] FA [auth D] GA [auth D] AA [auth B], CA [auth C], DA [auth C], FA [auth D], GA [auth D], W [auth A], X [auth A], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain Y [auth A] SDF format, chain HA [auth D] SDF format, chain EA [auth C] SDF format, chain BA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain EA [auth C] MOL2 format, chain BA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain EA [auth C] mmCIF format, chain BA [auth B]	BA [auth B], EA [auth C], HA [auth D], Y [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain EA [auth C] Focus chain HA [auth D] Focus chain Y [auth A] Interactions & Density Focus chain BA [auth B] Focus chain EA [auth C] Focus chain HA [auth D] Focus chain Y [auth A]