8G2K | pdb_00008g2k

Structure of the H3 hemagglutinin of A/California/7/2004

PDB DOI: https://doi.org/10.2210/pdb8G2K/pdb

Classification: VIRAL PROTEIN
Organism(s): Alphainfluenzavirus influenzae
Mutation(s): No

Deposited: 2023-02-05 Released: 2024-05-15
Deposition Author(s): Venkatramani, L., Mooers, B.H.M., Air, G.M.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.235 (Depositor), 0.237 (DCC)
R-Value Work:
0.209 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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Literature

Structure of the H3 hemagglutinin of A/California/7/2004

Venkatramani, L., Mooers, B.H.M., Air, G.M.

To be published.

Macromolecule Content

Total Structure Weight: 57.85 kDa
Atom Count: 4,177
Modeled Residue Count: 491
Deposited Residue Count: 491
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A	318	Alphainfluenzavirus influenzae	Mutation(s): 0
UniProt
Find proteins for H9XN76 (Influenza A virus) Explore H9XN76 Go to UniProtKB: H9XN76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H9XN76
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B	173	Alphainfluenzavirus influenzae	Mutation(s): 0
UniProt
Find proteins for A4GXQ1 (Influenza A virus) Explore A4GXQ1 Go to UniProtKB: A4GXQ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4GXQ1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B
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	C, E, F	2		N-Glycosylation	Interactions Focus chain C Focus chain E Focus chain F Interactions & Density Focus chain C Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B]	G [auth A], H [auth A], I [auth A], J [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.235 (Depositor), 0.237 (DCC)
R-Value Work: 0.209 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.199	α = 90
b = 101.199	β = 90
c = 384.462	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-15

Deposition Author(s):

Venkatramani, L.

Mooers, B.H.M.

Air, G.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	NIH 2P20GM103640
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM145423
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30 CA225520

Revision History (Full details and data files)

Version 1.0: 2024-05-15
Version 2.0: 2024-10-02
Type: Coordinate replacement
Reason: Chirality error
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
Version 2.1: 2024-10-16
Changes: Structure summary