6N08

Crystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2)

PDB DOI: https://doi.org/10.2210/pdb6N08/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Netherlands/209/1980(H3N2))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2018-11-06 Released: 2019-05-15
Deposition Author(s): Dai, Y.N., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.252
R-Value Work: 0.224
R-Value Observed: 0.225

Starting Model: experimental
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This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2)

Dai, Y.N., Fremont, D.H.

To be published.

Macromolecule Content

Total Structure Weight: 174.03 kDa
Atom Count: 13,045
Modelled Residue Count: 1,464
Deposited Residue Count: 1,491
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B, C	497	Influenza A virus (A/Netherlands/209/1980(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for H9XIV6 (Influenza A virus) Explore H9XIV6 Go to UniProtKB: H9XIV6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H9XIV6
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	D, F, G, H, J D, F, G, H, J, K, M	2		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain G Focus chain H Focus chain J Focus chain K Focus chain M Interactions & Density Focus chain D Focus chain F Focus chain G Focus chain H Focus chain J Focus chain K Focus chain M
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	E, I, L, N	3		N-Glycosylation	Interactions Focus chain E Focus chain I Focus chain L Focus chain N Interactions & Density Focus chain E Focus chain I Focus chain L Focus chain N
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C]	O [auth A] P [auth A] Q [auth A] R [auth B] S [auth C] O [auth A], P [auth A], Q [auth A], R [auth B], S [auth C], T [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.252
R-Value Work: 0.224
R-Value Observed: 0.225
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.99	α = 90
b = 188.77	β = 109.82
c = 108.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-05-15

Deposition Author(s):

Dai, Y.N.

Fremont, D.H.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary

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Help and Resources

6N08

Crystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2)

Crystal structure of hemagglutinin from influenza virus A/Netherlands/209/1980 (H3N2)

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)