6V46 | pdb_00006v46

The crystal structure of hemagglutinin from A/turkey/Ontario/6118/1968 (H8N4)

PDB DOI: https://doi.org/10.2210/pdb6V46/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/turkey/Ontario/6118/1968(H8N4))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2019-11-27 Released: 2020-06-17
Deposition Author(s): Yang, H., Stevens, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.225 (Depositor), 0.226 (DCC)
R-Value Work:
0.187 (Depositor), 0.188 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Molecular characterization and three-dimensional structures of avian H8, H11, H14, H15 and swine H4 influenza virus hemagglutinins

Yang, H., Carney, P.J., Chang, J., Stevens, J.

(2020) Heliyon 6: e04068

DOI: https://doi.org/10.1016/j.heliyon.2020.e04068

Macromolecule Content

Total Structure Weight: 177.84 kDa
Atom Count: 12,485
Modeled Residue Count: 1,467
Deposited Residue Count: 1,542
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A, C, E	331	Influenza A virus (A/turkey/Ontario/6118/1968(H8N4))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for P03456 (Influenza A virus (strain A/Turkey/Ontario/6118/1968 H8N4)) Explore P03456 Go to UniProtKB: P03456
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03456
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B, D, F	183	Influenza A virus (A/turkey/Ontario/6118/1968(H8N4))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for P03456 (Influenza A virus (strain A/Turkey/Ontario/6118/1968 H8N4)) Explore P03456 Go to UniProtKB: P03456
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03456
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, K	3		N-Glycosylation	Interactions Focus chain G Focus chain I Focus chain K Interactions & Density Focus chain G Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, J, L	2		N-Glycosylation	Interactions Focus chain H Focus chain J Focus chain L Interactions & Density Focus chain H Focus chain J Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 E] SDF format, chain N [auth C] SDF format, chain M [auth A] MOL2 format, chain O [auth E] MOL2 format, chain N [auth C] MOL2 format, chain M [auth A] mmCIF format, chain O [auth E] mmCIF format, chain N [auth C] mmCIF format, chain M [auth A]	M [auth A], N [auth C], O [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth C] Focus chain O [auth E] Interactions & Density Focus chain M [auth A] Focus chain N [auth C] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.225 (Depositor), 0.226 (DCC)
R-Value Work: 0.187 (Depositor), 0.188 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.047	α = 90
b = 98.086	β = 115.2
c = 132.735	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-06-17

Deposition Author(s):

Yang, H.

Stevens, J.

Revision History (Full details and data files)

Version 1.0: 2020-06-17
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: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary