4N5Y

Crystal structure of H5 hemagglutinin mutant (N158D, N224K and Q226L) from the influenza virus A/Viet Nam/1203/2004 (H5N1)

PDB DOI: https://doi.org/10.2210/pdb4N5Y/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus (A/Viet Nam/1203/2004(H5N1))
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2013-10-10 Released: 2013-11-20
Deposition Author(s): Zhu, X., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.16 Å
R-Value Free: 0.262
R-Value Work: 0.213
R-Value Observed: 0.215

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

Hemagglutinin Receptor Specificity and Structural Analyses of Respiratory Droplet-Transmissible H5N1 Viruses.

de Vries, R.P., Zhu, X., McBride, R., Rigter, A., Hanson, A., Zhong, G., Hatta, M., Xu, R., Yu, W., Kawaoka, Y., de Haan, C.A., Wilson, I.A., Paulson, J.C.

(2014) J Virol 88: 768-773

PubMed: 24173215 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JVI.02690-13
Primary Citation of Related Structures:
4N5Y, 4N5Z

PubMed Abstract:
Two ferret-adapted H5N1 viruses capable of respiratory droplet transmission have been reported with mutations in the hemagglutinin receptor-binding site and stalk domains. Glycan microarray analysis reveals that both viruses exhibit a strong shift toward binding to "human-type" α2-6 sialosides but with notable differences in fine specificity. Crystal structure analysis further shows that the stalk mutation causes no obvious perturbation of the receptor-binding pocket, consistent with its impact on hemagglutinin stability without affecting receptor specificity.

Organizational Affiliation

Departments of Cell and Molecular Biology and Chemical Physiology, The Scripps Research Institute, La Jolla, California, USA.

Macromolecule Content

Total Structure Weight: 895.69 kDa
Atom Count: 60,964
Modelled Residue Count: 7,515
Deposited Residue Count: 7,725
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 HA1 chain	A B [auth C] C [auth E] D [auth G] E [auth I] A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K], G [auth M], H [auth O], I [auth Q], J [auth S], K [auth U], L [auth W], M [auth Y], N [auth a], O [auth c]	334	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 3 Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33 Go to UniProtKB: Q6DQ33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6DQ33
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B [auth C] Focus chain C [auth E] Focus chain D [auth G] Focus chain E [auth I] Focus chain F [auth K] Focus chain G [auth M] Focus chain H [auth O] Focus chain I [auth Q] Focus chain J [auth S] Focus chain K [auth U] Focus chain L [auth W] Focus chain M [auth Y] Focus chain N [auth a] Focus chain O [auth c]
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 HA2 chain	AA [auth X] BA [auth Z] CA [auth b] DA [auth d] P [auth B] AA [auth X], BA [auth Z], CA [auth b], DA [auth d], P [auth B], Q [auth D], R [auth F], S [auth H], T [auth J], U [auth L], V [auth N], W [auth P], X [auth R], Y [auth T], Z [auth V]	181	Influenza A virus (A/Viet Nam/1203/2004(H5N1))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for Q6DQ33 (Influenza A virus (strain A/Vietnam/1203/2004 H5N1)) Explore Q6DQ33 Go to UniProtKB: Q6DQ33
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6DQ33
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	EA [auth e], GA [auth g], HA [auth h], JA [auth j], LA [auth l], EA [auth e], GA [auth g], HA [auth h], JA [auth j], LA [auth l], NA [auth n], OA [auth o], QA [auth q], WA [auth w], YA [auth y]	3		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain QA [auth q] Focus chain WA [auth w] Focus chain YA [auth y] Interactions & Density Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain LA [auth l] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain QA [auth q] Focus chain WA [auth w] Focus chain YA [auth y]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AB [auth 0], BB [auth 1], FA [auth f], IA [auth i], KA [auth k], AB [auth 0], BB [auth 1], FA [auth f], IA [auth i], KA [auth k], MA [auth m], PA [auth p], RA [auth r], TA [auth t], UA [auth u], VA [auth v], XA [auth x], ZA [auth z]	2		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain BB [auth 1] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain PA [auth p] Focus chain RA [auth r] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain VA [auth v] Focus chain XA [auth x] Focus chain ZA [auth z] Interactions & Density Focus chain AB [auth 0] Focus chain BB [auth 1] Focus chain FA [auth f] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain MA [auth m] Focus chain PA [auth p] Focus chain RA [auth r] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain VA [auth v] Focus chain XA [auth x] Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
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	SA [auth s]	4		N-Glycosylation	Interactions Focus chain SA [auth s] Interactions & Density Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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 CB [auth K] SDF format, chain DB [auth O] SDF format, chain EB [auth Y] SDF format, chain FB [auth c] SDF format, chain GB [auth c] MOL2 format, chain CB [auth K] MOL2 format, chain DB [auth O] MOL2 format, chain EB [auth Y] MOL2 format, chain FB [auth c] MOL2 format, chain GB [auth c] mmCIF format, chain CB [auth K] mmCIF format, chain DB [auth O] mmCIF format, chain EB [auth Y] mmCIF format, chain FB [auth c] mmCIF format, chain GB [auth c]	CB [auth K], DB [auth O], EB [auth Y], FB [auth c], GB [auth c]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CB [auth K] Focus chain DB [auth O] Focus chain EB [auth Y] Focus chain FB [auth c] Focus chain GB [auth c] Interactions & Density Focus chain CB [auth K] Focus chain DB [auth O] Focus chain EB [auth Y] Focus chain FB [auth c] Focus chain GB [auth c]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.16 Å
R-Value Free: 0.262
R-Value Work: 0.213
R-Value Observed: 0.215
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.915	α = 91.5
b = 118.105	β = 90.18
c = 273.799	γ = 119.87

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-11-20

Deposition Author(s):

Zhu, X.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2013-11-20
Type: Initial release
Version 1.1: 2014-01-01
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: 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: 2024-10-30
Changes: Structure summary