6Y5J

Dilated form 2 of X-31 Influenza Haemagglutinin at pH 5 (State III)

PDB DOI: https://doi.org/10.2210/pdb6Y5J/pdb
EM Map EMD-10699: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): unidentified influenza virus
Expression System: Gallus gallus
Mutation(s): No
Membrane Protein: Yes mpstruc

Deposited: 2020-02-25 Released: 2020-06-10
Deposition Author(s): Benton, D.J., Rosenthal, P.B.
Funding Organization(s): The Francis Crick Institute

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 5.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 169 kDa
Atom Count: 9,609
Modelled Residue Count: 1,185
Deposited Residue Count: 1,470
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
X-31 Influenza Haemagglutinin HA1	A, C, D [auth E]	318	unidentified influenza virus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2)) Explore P03437 Go to UniProtKB: P03437
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03437
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
X-31 Influenza Haemagglutinin HA2	B, E [auth D], F	172	unidentified influenza virus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P03437 (Influenza A virus (strain A/Aichi/2/1968 H3N2)) Explore P03437 Go to UniProtKB: P03437
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03437
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)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, K	3		N-Glycosylation	Interactions Focus chain G Focus chain I Focus chain K Interactions & Density Focus chain G Focus chain I Focus chain K
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	H, J, L	2		N-Glycosylation	Interactions Focus chain H Focus chain J Focus chain L Interactions & Density Focus chain H Focus chain J Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth E] SDF format, chain R [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E]	M [auth A] N [auth A] O [auth C] P [auth C] Q [auth E] M [auth A], N [auth A], O [auth C], P [auth C], Q [auth E], R [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth E] Focus chain R [auth E] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth E] Focus chain R [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 5.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	2

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-06-10

Deposition Author(s):

Benton, D.J.

Rosenthal, P.B.

Funding Organization	Location	Grant Number
The Francis Crick Institute	United Kingdom	FC001078
The Francis Crick Institute	United Kingdom	FC001143

Revision History (Full details and data files)

Version 1.0: 2020-06-10
Type: Initial release
Version 1.1: 2020-07-15
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

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Help and Resources

6Y5J

Dilated form 2 of X-31 Influenza Haemagglutinin at pH 5 (State III)

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2