4JUN | pdb_00004jun

Crystal structure of H5N1 influenza virus hemagglutinin, clade 5

PDB DOI: https://doi.org/10.2210/pdb4JUN/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/duck/Guangxi/2396/2004(H5N1))
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2013-03-25 Released: 2014-05-07
Deposition Author(s): DuBois, R.M., Zaraket, H., Reddivari, M., Coop, T., Heath, R.J., White, S.W., Russell, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.245 (Depositor), 0.242 (DCC)
R-Value Work:
0.201 (Depositor), 0.197 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

To be published

DuBois, R.M., Zaraket, H., Reddivari, M., Coop, T., Heath, R.J., White, S.W., Russell, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 175.9 kDa
Atom Count: 12,083
Modeled Residue Count: 1,463
Deposited Residue Count: 1,533
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1	A, C, E	329	Influenza A virus (A/duck/Guangxi/2396/2004(H5N1))	Mutation(s): 0 Gene Names: HA, hemagglutinin
UniProt
Find proteins for Q2F4V6 (Influenza A virus) Explore Q2F4V6 Go to UniProtKB: Q2F4V6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2F4V6
Glycosylation
Glycosylation Sites: 2	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	B, D, F	182	Influenza A virus (A/duck/Guangxi/2396/2004(H5N1))	Mutation(s): 0 Gene Names: HA, hemagglutinin
UniProt
Find proteins for Q2F4V6 (Influenza A virus) Explore Q2F4V6 Go to UniProtKB: Q2F4V6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2F4V6
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I	2		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Interactions & Density Focus chain G Focus chain H Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain M [auth E] MOL2 format, chain M [auth E] mmCIF format, chain M [auth E]	M [auth E]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Interactions & Density Focus chain M [auth E]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain K [auth C] SDF format, chain J [auth A] MOL2 format, chain L [auth E] MOL2 format, chain K [auth C] MOL2 format, chain J [auth A] mmCIF format, chain L [auth E] mmCIF format, chain K [auth C] mmCIF format, chain J [auth A]	J [auth A], K [auth C], L [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth E] Interactions & Density Focus chain J [auth A] Focus chain K [auth C] Focus chain L [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.245 (Depositor), 0.242 (DCC)
R-Value Work: 0.201 (Depositor), 0.197 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.036	α = 90
b = 237.056	β = 119.18
c = 72.857	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-05-07
Type: Initial release
Version 1.1: 2014-11-19
Changes: Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary