8US0 | pdb_00008us0

Human antibody S8V1-157 in complex with the A/American black duck/New Brunswick/00464/2010(H4N6) HA head domain

PDB DOI: https://doi.org/10.2210/pdb8US0/pdb

Classification: Viral Protein/IMMUNE SYSTEM
Organism(s): Influenza A virus, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-10-27 Released: 2024-10-30
Deposition Author(s): McCarthy, K.R.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free:
0.293 (Depositor), 0.283 (DCC)
R-Value Work:
0.246 (Depositor), 0.242 (DCC)
R-Value Observed:
0.248 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A protective and broadly binding antibody class engages the influenza virus hemagglutinin head at its stem interface.

Simmons, H.C., Finney, J., Kotaki, R., Adachi, Y., Park Moseman, A., Watanabe, A., Song, S., Robinson-McCarthy, L.R., Le Sage, V., Kuraoka, M., Moseman, E.A., Kelsoe, G., Takahashi, Y., McCarthy, K.R.

(2024) bioRxiv

PubMed: 38168412 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1101/2023.12.13.571543
Primary Citation Related Structures:
8US0

PubMed Abstract:
Influenza infection and vaccination impart strain-specific immunity that protects against neither seasonal antigenic variants nor the next pandemic. However, antibodies directed to conserved sites can confer broad protection. Here we identify and characterize a class of human antibodies that engage a previously undescribed, conserved epitope on the influenza hemagglutinin (HA) protein. Prototype antibody S8V1-157 binds at the normally occluded interface between the HA head and stem. Antibodies to this HA head-stem interface epitope are non-neutralizing in vitro but protect against lethal influenza infection in mice. Antibody isotypes that direct clearance of infected cells enhance this protection. Head-stem interface antibodies bind to most influenza A serotypes and seasonal human variants, and are present at low frequencies in the memory B cell populations of multiple human donors. Vaccines designed to elicit these antibodies might contribute to "universal" influenza immunity.

Organizational Affiliation

Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

Macromolecule Content

Total Structure Weight: 494.58 kDa
Atom Count: 33,101
Modeled Residue Count: 4,244
Deposited Residue Count: 4,464
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A B [auth D] C [auth G] D [auth J] E [auth M] A, B [auth D], C [auth G], D [auth J], E [auth M], F [auth P]	292	Influenza A virus	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for M1UPL4 (Influenza A virus) Explore M1UPL4 Go to UniProtKB: M1UPL4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M1UPL4
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B [auth D] Focus chain C [auth G] Focus chain D [auth J] Focus chain E [auth M] Focus chain F [auth P]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
human antibody S8V1-157 light chain	G [auth O] H [auth I] I [auth C] J [auth R] K [auth F] G [auth O], H [auth I], I [auth C], J [auth R], K [auth F], R [auth L]	221	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
human antibody S8V1-157 heavy chain	L [auth B] M [auth H] N [auth K] O [auth N] P [auth Q] L [auth B], M [auth H], N [auth K], O [auth N], P [auth Q], Q [auth E]	231	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], CA [auth c], S, T, U, AA [auth a], CA [auth c], S, T, U, V, W, X	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], Y, Z	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain Y Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain HA [auth M] MOL2 format, chain HA [auth M] mmCIF format, chain HA [auth M]	HA [auth M]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain HA [auth M] Interactions & Density Focus chain HA [auth M]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain JA [auth P] SDF format, chain IA [auth M] SDF format, chain GA [auth J] SDF format, chain FA [auth G] SDF format, chain EA [auth D] SDF format, chain DA [auth A] MOL2 format, chain JA [auth P] MOL2 format, chain IA [auth M] MOL2 format, chain GA [auth J] MOL2 format, chain FA [auth G] MOL2 format, chain EA [auth D] MOL2 format, chain DA [auth A] mmCIF format, chain JA [auth P] mmCIF format, chain IA [auth M] mmCIF format, chain GA [auth J] mmCIF format, chain FA [auth G] mmCIF format, chain EA [auth D] mmCIF format, chain DA [auth A]	DA [auth A] EA [auth D] FA [auth G] GA [auth J] IA [auth M] DA [auth A], EA [auth D], FA [auth G], GA [auth J], IA [auth M], JA [auth P]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain EA [auth D] Focus chain FA [auth G] Focus chain GA [auth J] Focus chain IA [auth M] Focus chain JA [auth P] Interactions & Density Focus chain DA [auth A] Focus chain EA [auth D] Focus chain FA [auth G] Focus chain GA [auth J] Focus chain IA [auth M] Focus chain JA [auth P]