3SAL

Crystal Structure of Influenza A Virus Neuraminidase N5

PDB DOI: https://doi.org/10.2210/pdb3SAL/pdb

Classification: HYDROLASE
Organism(s): Influenza A virus (A/duck/Alberta/60/1976(H12N5))
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2011-06-03 Released: 2011-08-10
Deposition Author(s): Wang, M.Y., Qi, J.X., Liu, Y., Vavricka, C.J., Wu, Y., Li, Q., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.164
R-Value Work: 0.126
R-Value Observed: 0.128

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Influenza a virus n5 neuraminidase has an extended 150-cavity

Wang, M.Y., Qi, J.X., Liu, Y., Vavricka, C.J., Wu, Y., Li, Q., Gao, G.F.

(2011) J Virol 85: 8431-8435

PubMed: 21653672 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JVI.00638-11
Primary Citation of Related Structures:
3SAL, 3SAN

PubMed Abstract:
There are 9 serotypes of neuraminidase (NA) from influenza A virus (N1 to N9), which are classified into two groups based on primary sequences (groups 1 and 2). The structural hallmark of the two groups is the presence or absence of an extra 150-cavity (formed by the 150-loop) in the active site. Thus far, structures of NAs from 6 out of the 9 serotypes have been solved. Here, we solved the N5 structure, the last unknown structure group 1 serotype with a unique Asn147 residue in its 150-loop, demonstrating that it has an extended 150-cavity that closes upon inhibitor binding.

Organizational Affiliation

CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, The People's Republic of China. gaof@im.ac.cn

Macromolecule Content

Total Structure Weight: 89.63 kDa
Atom Count: 7,225
Modelled Residue Count: 788
Deposited Residue Count: 790
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A, B	395	Influenza A virus (A/duck/Alberta/60/1976(H12N5))	Mutation(s): 0 Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for A1ILL9 (Influenza A virus (strain A/Duck/Alberta/60/1976 H12N5)) Explore A1ILL9 Go to UniProtKB: A1ILL9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1ILL9
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation	Interactions Focus chain C Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
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	D, F	3		N-Glycosylation	Interactions Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.164
R-Value Work: 0.126
R-Value Observed: 0.128
Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.513	α = 90
b = 111.513	β = 90
c = 66.465	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-08-10
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary