9B7I | pdb_00009b7i

Crystal structure of the H3 hemagglutinin COBRA J4

PDB DOI: https://doi.org/10.2210/pdb9B7I/pdb

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

Deposited: 2024-03-27 Released: 2025-05-07
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: 2.90 Å
R-Value Free:
0.285 (Depositor), 0.285 (DCC)
R-Value Work:
0.228 (Depositor), 0.228 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Assessing the structural boundaries of broadly reactive antibody interactions with diverse H3 influenza hemagglutinin proteins

Dzimianski, J.V., Nagashima, K.A., Cruz, J.M., Sautto, G.A., O'Rourke, S.M., Serrao, V.B.H., Ross, T.M., Mousa, J.J., DuBois, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 357.83 kDa
Atom Count: 24,328
Modeled Residue Count: 2,934
Deposited Residue Count: 3,024
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	A, B, C, D, E A, B, C, D, E, F	323	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A5J6A4B5 (Influenza A virus) Explore A0A5J6A4B5 Go to UniProtKB: A0A5J6A4B5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5J6A4B5
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F
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	G [auth a] H [auth b] I [auth c] J [auth d] K [auth e] G [auth a], H [auth b], I [auth c], J [auth d], K [auth e], L [auth f]	181	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for A0A5J6UNG5 (Influenza A virus) Explore A0A5J6UNG5 Go to UniProtKB: A0A5J6UNG5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5J6UNG5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain G [auth a] Focus chain I [auth c] Focus chain J [auth d] Focus chain L [auth f]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
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	M [auth G], Q [auth K], U [auth O]	4		N-Glycosylation	Interactions Focus chain M [auth G] Focus chain Q [auth K] Focus chain U [auth O] Interactions & Density Focus chain M [auth G] Focus chain Q [auth K] Focus chain U [auth O]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 4
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 X], N [auth H], O [auth I], Z [auth T]	4		N-Glycosylation	Interactions Focus chain DA [auth X] Focus chain N [auth H] Focus chain O [auth I] Focus chain Z [auth T] Interactions & Density Focus chain DA [auth X] Focus chain N [auth H] Focus chain O [auth I] Focus chain Z [auth T]
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 5
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	P [auth J], R [auth L], V [auth P], X [auth R], Y [auth S]	3		N-Glycosylation	Interactions Focus chain P [auth J] Focus chain R [auth L] Focus chain V [auth P] Focus chain X [auth R] Focus chain Y [auth S] Interactions & Density Focus chain P [auth J] Focus chain R [auth L] Focus chain V [auth P] Focus chain X [auth R] Focus chain Y [auth S]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	AA [auth U], BA [auth V], S [auth M], T [auth N]	5		N-Glycosylation	Interactions Focus chain AA [auth U] Focus chain BA [auth V] Focus chain S [auth M] Focus chain T [auth N] Interactions & Density Focus chain AA [auth U] Focus chain BA [auth V] Focus chain S [auth M] Focus chain T [auth N]
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	CA [auth W], EA [auth Y], W [auth Q]	2		N-Glycosylation	Interactions Focus chain CA [auth W] Focus chain EA [auth Y] Focus chain W [auth Q] Interactions & Density Focus chain CA [auth W] Focus chain EA [auth Y] Focus chain W [auth Q]
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 FA [auth A] SDF format, chain GA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth D] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain SA [auth F] SDF format, chain TA [auth a] SDF format, chain UA [auth c] SDF format, chain VA [auth d] SDF format, chain WA [auth f] SDF format, chain HA [auth A] SDF format, chain PA [auth E] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth F] MOL2 format, chain TA [auth a] MOL2 format, chain UA [auth c] MOL2 format, chain VA [auth d] MOL2 format, chain WA [auth f] MOL2 format, chain HA [auth A] MOL2 format, chain PA [auth E] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth D] mmCIF format, chain QA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain SA [auth F] mmCIF format, chain TA [auth a] mmCIF format, chain UA [auth c] mmCIF format, chain VA [auth d] mmCIF format, chain WA [auth f] mmCIF format, chain HA [auth A] mmCIF format, chain PA [auth E]	FA [auth A] GA [auth A] HA [auth A] IA [auth A] JA [auth B] FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth B], KA [auth B], LA [auth C], MA [auth C], NA [auth C], OA [auth D], PA [auth E], QA [auth E], RA [auth E], SA [auth F], TA [auth a], UA [auth c], VA [auth d], WA [auth f]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth D] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth F] Focus chain TA [auth a] Focus chain UA [auth c] Focus chain VA [auth d] Focus chain WA [auth f] Interactions & Density Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth D] Focus chain PA [auth E] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain SA [auth F] Focus chain TA [auth a] Focus chain UA [auth c] Focus chain VA [auth d] Focus chain WA [auth f]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.285 (Depositor), 0.285 (DCC)
R-Value Work: 0.228 (Depositor), 0.228 (DCC)
R-Value Observed: 0.231 (Depositor)

Diffraction Data: https://doi.org/10.18430/M39B7I

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.744	α = 71.61
b = 105.304	β = 73.38
c = 109.682	γ = 87.07

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
DIALS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-07

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: 2025-05-07
Type: Initial release

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Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9B7I | pdb_00009b7i

Crystal structure of the H3 hemagglutinin COBRA J4

Assessing the structural boundaries of broadly reactive antibody interactions with diverse H3 influenza hemagglutinin proteins

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

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

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

9B7I | pdb_00009b7i