8ZR4 | pdb_00008zr4

Cryo-EM structure of the N2-4N2C402 complex at a resolution of 1.9 angstrom

PDB DOI: https://doi.org/10.2210/pdb8ZR4/pdb
EM Map EMD-60391: EMDB EMDataResource

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

Deposited: 2024-06-03 Released: 2025-01-01
Deposition Author(s): Chu, B.X., Wang, X., Yang, Q., Wu, X.D., Zhang, Z.L.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Profiling influenza neuraminidase pre-existing humoral immunity in humans

Wang, X., Yang, Q., Chu, B.X., Wu, X.D., Zhang, Z.L.

(2024) Cell Host Microbe

Macromolecule Content

Total Structure Weight: 289.22 kDa
Atom Count: 20,526
Modeled Residue Count: 2,488
Deposited Residue Count: 2,564
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4N2C402_Fab_H	A, D [auth F], G [auth I], J [auth L]	135	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
4N2C402_Fab_L	B, E [auth G], H [auth J], K [auth M]	113	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	C [auth D], F [auth H], I [auth K], L [auth N]	393	Influenza A virus	Mutation(s): 0 Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for A0A2S0X6Y5 (Influenza A virus) Explore A0A2S0X6Y5 Go to UniProtKB: A0A2S0X6Y5
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2S0X6Y5
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Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	M [auth O], N [auth P], O [auth Q], P [auth R]	5		N/A	Interactions Focus chain M [auth O] Focus chain N [auth P] Focus chain O [auth Q] Focus chain P [auth R] Interactions & Density Focus chain M [auth O] Focus chain N [auth P] Focus chain O [auth Q] Focus chain P [auth R]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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 AA [auth N] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain T [auth H] SDF format, chain U [auth H] SDF format, chain W [auth K] SDF format, chain X [auth K] SDF format, chain Z [auth N] MOL2 format, chain AA [auth N] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain T [auth H] MOL2 format, chain U [auth H] MOL2 format, chain W [auth K] MOL2 format, chain X [auth K] MOL2 format, chain Z [auth N] mmCIF format, chain AA [auth N] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain T [auth H] mmCIF format, chain U [auth H] mmCIF format, chain W [auth K] mmCIF format, chain X [auth K] mmCIF format, chain Z [auth N]	AA [auth N] Q [auth D] R [auth D] T [auth H] U [auth H] AA [auth N], Q [auth D], R [auth D], T [auth H], U [auth H], W [auth K], X [auth K], Z [auth N]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth N] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth H] Focus chain U [auth H] Focus chain W [auth K] Focus chain X [auth K] Focus chain Z [auth N] Interactions & Density Focus chain AA [auth N] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth H] Focus chain U [auth H] Focus chain W [auth K] Focus chain X [auth K] Focus chain Z [auth N]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth N] SDF format, chain S [auth D] SDF format, chain V [auth H] SDF format, chain Y [auth K] MOL2 format, chain BA [auth N] MOL2 format, chain S [auth D] MOL2 format, chain V [auth H] MOL2 format, chain Y [auth K] mmCIF format, chain BA [auth N] mmCIF format, chain S [auth D] mmCIF format, chain V [auth H] mmCIF format, chain Y [auth K]	BA [auth N], S [auth D], V [auth H], Y [auth K]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth N] Focus chain S [auth D] Focus chain V [auth H] Focus chain Y [auth K] Interactions & Density Focus chain BA [auth N] Focus chain S [auth D] Focus chain V [auth H] Focus chain Y [auth K]