7UYI

Crystal structure of the computationally optimized broadly reactive H1 influenza hemagglutinin P1

PDB DOI: https://doi.org/10.2210/pdb7UYI/pdb

Classification: VIRAL PROTEIN
Organism(s): Influenza A virus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2022-05-06 Released: 2023-04-19
Deposition Author(s): Dzimianski, J.V., DuBois, R.M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.270
R-Value Work: 0.226
R-Value Observed: 0.228

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine

Dzimianski, J.V., Han, J., Sautto, G.A., O’Rourke, S.M., Cruz, J.M., Pierce, S.R., Ecker, J.W., Carlock, M.A., Nagashima, K.A., Mousa, J.J., Ross, T.M., Ward, A.B., DuBois, R.M.

(2023) Commun Biol 6: 454

DOI: https://doi.org/10.1038/s42003-023-04793-3

Macromolecule Content

Total Structure Weight: 356.48 kDa
Atom Count: 23,338
Modelled Residue Count: 2,852
Deposited Residue Count: 3,078
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COBRA P1 HA	A B C D [auth E] E [auth F] A, B, C, D [auth E], E [auth F], F [auth D]	513	Influenza A virus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
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	G, P	4	N/A	N-Glycosylation	Interactions Focus chain G Focus chain P Interactions & Density Focus chain G Focus chain P
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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	H, I, K, O, Q	2	N/A	N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain K Focus chain O Focus chain Q Interactions & Density Focus chain H Focus chain I Focus chain K Focus chain O Focus chain Q
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
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	J, L, M	3	N/A	N-Glycosylation	Interactions Focus chain J Focus chain L Focus chain M Interactions & Density Focus chain J Focus chain L Focus chain M
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
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	N, R	5	N/A	N-Glycosylation	Interactions Focus chain N Focus chain R Interactions & Density Focus chain N Focus chain R
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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 AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth E] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth E] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth E], FA [auth F], GA [auth F], HA [auth D], IA [auth D], JA [auth D], KA [auth D], S [auth A], T [auth A], U [auth A], V [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth E] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.270
R-Value Work: 0.226
R-Value Observed: 0.228
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.18430/M37UYI

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 264.849	α = 90
b = 77.56	β = 93.773
c = 222.523	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
DIALS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-19

Deposition Author(s):

Dzimianski, J.V.

DuBois, R.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93019C00052

Revision History (Full details and data files)

Version 1.0: 2023-04-19
Type: Initial release
Version 1.1: 2023-05-03
Changes: Database references

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7UYI

Crystal structure of the computationally optimized broadly reactive H1 influenza hemagglutinin P1

Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)