6CRD

INFLUENZA VIRUS NEURAMINIDASE SUBTYPE N9 (TERN) with tetrabrachion (TB) domain stalk

PDB DOI: https://doi.org/10.2210/pdb6CRD/pdb

Classification: viral protein/hydrolase
Organism(s): Staphylothermus marinus, Influenza A virus (A/tern/Australia/G70C/1975(H11N9))
Expression System: Insect cell expression vector pTIE1
Mutation(s): No

Deposited: 2018-03-16 Released: 2019-01-23
Deposition Author(s): Streltsov, V.A., Schmidt, P., McKimm-Breschkin, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.306
R-Value Work: 0.208
R-Value Observed: 0.213

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structure of an Influenza A virus N9 neuraminidase with a tetrabrachion-domain stalk.

Streltsov, V.A., Schmidt, P.M., McKimm-Breschkin, J.L.

(2019) Acta Crystallogr F Struct Biol Commun 75: 89-97

PubMed: 30713159 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X18017892
Primary Citation of Related Structures:
6CRD, 6D3B, 6MCX

PubMed Abstract:
The influenza neuraminidase (NA) is a homotetramer with head, stalk, transmembrane and cytoplasmic regions. The structure of the NA head with a stalk has never been determined. The NA head from an N9 subtype influenza A virus, A/tern/Australia/G70C/1975 (H1N9), was expressed with an artificial stalk derived from the tetrabrachion (TB) tetramerization domain from Staphylothermus marinus. The NA was successfully crystallized both with and without the TB stalk, and the structures were determined to 2.6 and 2.3 Å resolution, respectively. Comparisons of the two NAs with the native N9 NA structure from egg-grown virus showed that the artificial TB stalk maintained the native NA head structure, supporting previous biological observations.

Organizational Affiliation

CSIRO Manufacturing, 343 Royal Parade, Parkville, Victoria 3052, Australia.

Macromolecule Content

Total Structure Weight: 448.53 kDa
Atom Count: 29,975
Modelled Residue Count: 3,492
Deposited Residue Count: 3,784
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetrabrachion,Neuraminidase	A, B, C, D, E A, B, C, D, E, F, G, H	473	Staphylothermus marinus, Influenza A virus (A/tern/Australia/G70C/1975(H11N9))	Mutation(s): 0 EC: 3.2.1.18
UniProt
Find proteins for P03472 (Influenza A virus (strain A/Tern/Australia/G70C/1975 H11N9)) Explore P03472 Go to UniProtKB: P03472
Find proteins for Q54436 (Staphylothermus marinus) Explore Q54436 Go to UniProtKB: Q54436
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q54436P03472
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	CA [auth c], I, L, N, Q, CA [auth c], I, L, N, Q, T, W, Z	9		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain I Focus chain L Focus chain N Focus chain Q Focus chain T Focus chain W Focus chain Z Interactions & Density Focus chain CA [auth c] Focus chain I Focus chain L Focus chain N Focus chain Q Focus chain T Focus chain W Focus chain Z
Glycosylation Resources
GlyTouCan: G68668TB GlyCosmos: G68668TB GlyGen: G68668TB

Entity ID: 3
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], BA [auth b], DA [auth d], EA [auth e], J, AA [auth a], BA [auth b], DA [auth d], EA [auth e], J, M, O, P, R, S, U, V, X, Y	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain J Focus chain M Focus chain O Focus chain P Focus chain R Focus chain S Focus chain U Focus chain V Focus chain X Focus chain Y Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain J Focus chain M Focus chain O Focus chain P Focus chain R Focus chain S Focus chain U Focus chain V Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K	4		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth C] SDF format, chain JA [auth E] SDF format, chain KA [auth F] SDF format, chain LA [auth G] SDF format, chain MA [auth H] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth H] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth F] mmCIF format, chain LA [auth G] mmCIF format, chain MA [auth H]	FA [auth A] GA [auth B] HA [auth B] IA [auth C] JA [auth E] FA [auth A], GA [auth B], HA [auth B], IA [auth C], JA [auth E], KA [auth F], LA [auth G], MA [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FA [auth A] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth C] Focus chain JA [auth E] Focus chain KA [auth F] Focus chain LA [auth G] Focus chain MA [auth H] Interactions & Density Focus chain FA [auth A] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth C] Focus chain JA [auth E] Focus chain KA [auth F] Focus chain LA [auth G] Focus chain MA [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.306
R-Value Work: 0.208
R-Value Observed: 0.213
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.998	α = 90
b = 142.326	β = 91.48
c = 163.303	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Streltsov, V.A.

Schmidt, P.

McKimm-Breschkin, J.

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2019-11-13
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary