5XRT

Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb5XRT/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2)), Influenza A virus (A/swine/Indiana/A01260280/2013(H3N2))
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2017-06-09 Released: 2018-07-25
Deposition Author(s): Zhang, H., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.246
R-Value Work: 0.199
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 246.79 kDa
Atom Count: 16,943
Modelled Residue Count: 1,972
Deposited Residue Count: 2,012
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, C, E, G	329	Influenza A virus (A/swine/Minnesota/A01134337/2010(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for I0AXC3 (Influenza A virus) Explore I0AXC3 Go to UniProtKB: I0AXC3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I0AXC3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	B, D, F, H	174	Influenza A virus (A/swine/Indiana/A01260280/2013(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for R9XUW5 (Influenza A virus) Explore R9XUW5 Go to UniProtKB: R9XUW5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	R9XUW5
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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)-[beta-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I	5		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G31349EA GlyCosmos: G31349EA

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	J, K, P	4		N-Glycosylation	Interactions Focus chain J Focus chain K Focus chain P Interactions & Density Focus chain J Focus chain K Focus chain P
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L, Q, W	6		N-Glycosylation	Interactions Focus chain L Focus chain Q Focus chain W Interactions & Density Focus chain L Focus chain Q Focus chain W
Glycosylation Resources
GlyTouCan: G36544AC GlyCosmos: G36544AC GlyGen: G36544AC

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	EA [auth e], M, U, X	5		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain M Focus chain U Focus chain X Interactions & Density Focus chain EA [auth e] Focus chain M Focus chain U Focus chain X
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], N, S, Z	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain N Focus chain S Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain N Focus chain S Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
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	O, R	3		N-Glycosylation	Interactions Focus chain O Focus chain R Interactions & Density Focus chain O Focus chain R
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-L-fucopyranose-(1-3)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	T	3		N-Glycosylation	Interactions Focus chain T Interactions & Density Focus chain T
Glycosylation Resources
GlyTouCan: G55658LR GlyCosmos: G55658LR GlyGen: G55658LR

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-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	V	5		N-Glycosylation	Interactions Focus chain V Interactions & Density Focus chain V
Glycosylation Resources
GlyTouCan: G78750JU GlyCosmos: G78750JU GlyGen: G78750JU

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	Y	3		N-Glycosylation	Interactions Focus chain Y Interactions & Density Focus chain Y
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a]	5		N-Glycosylation	Interactions Focus chain AA [auth a] Interactions & Density Focus chain AA [auth a]
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Entity ID: 13
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c]	7		N-Glycosylation	Interactions Focus chain CA [auth c] Interactions & Density Focus chain CA [auth c]
Glycosylation Resources
GlyTouCan: G84676UY GlyCosmos: G84676UY GlyGen: G84676UY

Entity ID: 14
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	DA [auth d]	4		N-Glycosylation	Interactions Focus chain DA [auth d] Interactions & Density Focus chain DA [auth d]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 2 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 IA [auth C] SDF format, chain JA [auth D] 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 IA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth F] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth H]	FA [auth A] GA [auth B] IA [auth C] JA [auth D] KA [auth F] FA [auth A], GA [auth B], IA [auth C], JA [auth D], 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 IA [auth C] Focus chain JA [auth D] 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 IA [auth C] Focus chain JA [auth D] Focus chain KA [auth F] Focus chain LA [auth G] Focus chain MA [auth H]
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain HA [auth B] MOL2 format, chain HA [auth B]	HA [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain HA [auth B] Interactions & Density Focus chain HA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free: 0.246
R-Value Work: 0.199
R-Value Observed: 0.201
Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 292.782	α = 90
b = 292.782	β = 90
c = 292.782	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-07-25

Deposition Author(s):

Zhang, H.

Wilson, I.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U19 AI117905

Revision History (Full details and data files)

Version 1.0: 2018-07-25
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence, Data collection
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2022-10-12
Changes: Database references, Structure summary
Version 2.2: 2022-11-16
Changes: Other
Version 2.3: 2023-10-18
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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5XRT

Crystal structure of A/Minnesota/11/2010 (H3N2) influenza virus hemagglutinin

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

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Sequence Annotations

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Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Entity ID: 12

Glycosylation Resources

Entity ID: 13

Glycosylation Resources

Entity ID: 14

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)