4YY1 | pdb_00004yy1

The structure of hemagglutinin from a H6N1 influenza virus (A/chicken/Taiwan/A2837/2013) in complex with human receptor analog 6'SLNLN

PDB DOI: https://doi.org/10.2210/pdb4YY1/pdb

Classification: IMMUNE SYSTEM
Organism(s): H6N1 subtype
Expression System: Insect cell expression vector pTIE1
Mutation(s): No

Deposited: 2015-03-23 Released: 2016-03-23
Deposition Author(s): Wang, F., Qi, J., Bi, Y., Zhang, W., Wang, M., Wang, M., Liu, J., Yan, J., Shi, Y., Gao, G.F.
Funding Organization(s): China Ministry of Science and Technology National 973 Project, Intramural Special Grant for Influenza Virus Research from the Chinese Academy of Sciences, Intramural Special Grant for Strategic Priority Research Program of the Chinese Academy of Sciences, National Natural Science Foundation of China, China National Grand S&T Special Project

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.254 (Depositor), 0.245 (DCC)
R-Value Work:
0.210 (Depositor), 0.203 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure of hemagglutinin from a H6N1 influenza virus (A/chicken/Taiwan/A2837/2013)

Wang, F., Qi, J., Bi, Y., Zhang, W., Wang, M., Wang, M., Liu, J., Yan, J., Shi, Y., Gao, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 113.21 kDa
Atom Count: 7,944
Modeled Residue Count: 978
Deposited Residue Count: 978
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HA1	A, C	325	H6N1 subtype	Mutation(s): 0
UniProt
Find proteins for A0A0J9X268 (H6N1 subtype) Explore A0A0J9X268 Go to UniProtKB: A0A0J9X268
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0J9X268
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain 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
HA2	B, D	164	H6N1 subtype	Mutation(s): 0
UniProt
Find proteins for A0A0J9X267 (H6N1 subtype) Explore A0A0J9X267 Go to UniProtKB: A0A0J9X267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0J9X267
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G	2		N-Glycosylation	Interactions Focus chain E Focus chain G Interactions & Density Focus chain E Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose	F, H	2		N/A	Interactions Focus chain F Focus chain H Interactions & Density Focus chain F Focus chain H
Glycosylation Resources
GlyTouCan: G63069TR GlyCosmos: G63069TR GlyGen: G63069TR

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 I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	I [auth A], J [auth B], K [auth C], L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.254 (Depositor), 0.245 (DCC)
R-Value Work: 0.210 (Depositor), 0.203 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.06	α = 90
b = 97.06	β = 90
c = 131.649	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data processing
PHASER	phasing
Coot	model building
SCALA	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-03-23

Deposition Author(s):

Funding Organization	Location	Grant Number
China Ministry of Science and Technology National 973 Project	China	2011CB504703
Intramural Special Grant for Influenza Virus Research from the Chinese Academy of Sciences	China	KJZD-EW-L09
Intramural Special Grant for Strategic Priority Research Program of the Chinese Academy of Sciences	China	XDB08020100
National Natural Science Foundation of China	China	31402196
China National Grand S&T Special Project	China	2014ZX10004002

Revision History (Full details and data files)

Version 1.0: 2016-03-23
Type: Initial release
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: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary