4O58 | pdb_00004o58

Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/3/1975 (H3N2) influenza hemagglutinin

PDB DOI: https://doi.org/10.2210/pdb4O58/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Influenza A virus (A/Victoria/3/1975(H3N2)), Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2013-12-19 Released: 2014-04-16
Deposition Author(s): Lee, P.S., Wilson, I.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.224 (Depositor), 0.214 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus.

Lee, P.S., Ohshima, N., Stanfield, R.L., Yu, W., Iba, Y., Okuno, Y., Kurosawa, Y., Wilson, I.A.

(2014) Nat Commun 5: 3614-3614

PubMed: 24717798 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/ncomms4614
Primary Citation Related Structures:
4O58, 4O5I, 4O5L, 4O5N

PubMed Abstract:
Influenza viruses present a significant health challenge each year, as in the H3N2 epidemic of 2012-2013. Here we describe an antibody, F045-092, that possesses broadly neutralizing activity against the entire H3 subtype and accommodates the natural variation and additional glycosylation in all strains tested from 1963 to 2011. Crystal structures of F045-092 in complex with HAs from 1975 and 2011 H3N2 viruses reveal the structural basis for its neutralization breadth through insertion of its 23-residue HCDR3 into the receptor-binding site that involves striking receptor mimicry. F045-092 extends its recognition to divergent subtypes, including H1, H2 and H13, using the enhanced avidity of its IgG to overcome lower-affinity Fab binding, as observed with other antibodies that target the receptor-binding site. This unprecedented level of antibody cross-reactivity against the H3 subtype can potentially inform on development of a pan-H3 vaccine or small-molecule therapeutics.

Organizational Affiliation

1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA [2] The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Macromolecule Content

Total Structure Weight: 107.89 kDa
Atom Count: 7,390
Modeled Residue Count: 925
Deposited Residue Count: 955
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA1 chain	A	323	Influenza A virus (A/Victoria/3/1975(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for P03435 (Influenza A virus (strain A/Victoria/3/1975 H3N2)) Explore P03435 Go to UniProtKB: P03435
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03435
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin HA2 chain	B	176	Influenza A virus (A/Victoria/3/1975(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for P03435 (Influenza A virus (strain A/Victoria/3/1975 H3N2)) Explore P03435 Go to UniProtKB: P03435
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03435
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab F045-092 light chain	C [auth L]	216	Homo sapiens	Mutation(s): 0 Gene Names: IGL@, IGLC2
UniProt & NIH Common Fund Data Resources
Find proteins for P0DOY2 (Homo sapiens) Explore P0DOY2 Go to UniProtKB: P0DOY2
GTEx: ENSG00000211677
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DOY2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab F045-092 heavy chain	D [auth H]	240	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6C4S0 (Homo sapiens) Explore S6C4S0 Go to UniProtKB: S6C4S0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S6C4S0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	E [auth C], G [auth E]	2		N-Glycosylation	Interactions Focus chain E [auth C] Focus chain G [auth E] Interactions & Density Focus chain E [auth C] Focus chain G [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	F [auth D]	5		N-Glycosylation	Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B]	H [auth A], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain U [auth L] SDF format, chain V [auth L] MOL2 format, chain N [auth A] MOL2 format, chain U [auth L] MOL2 format, chain V [auth L] mmCIF format, chain N [auth A] mmCIF format, chain U [auth L] mmCIF format, chain V [auth L]	N [auth A], U [auth L], V [auth L]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain U [auth L] Focus chain V [auth L] Interactions & Density Focus chain N [auth A] Focus chain U [auth L] Focus chain V [auth L]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth L] SDF format, chain T [auth L] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain Z [auth H] SDF format, chain Y [auth H] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth L] MOL2 format, chain T [auth L] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth H] MOL2 format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth L] mmCIF format, chain T [auth L] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth H] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], P [auth B], Q [auth B], R [auth B], S [auth L], T [auth L], W [auth H], X [auth H], Y [auth H], Z [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth L] Focus chain T [auth L] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth L] Focus chain T [auth L] Focus chain W [auth H] Focus chain X [auth H] Focus chain Y [auth H] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.224 (Depositor), 0.214 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.180 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.101	α = 90
b = 99.101	β = 90
c = 336.65	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-04-16

Deposition Author(s):

Lee, P.S.

Wilson, I.A.

Revision History (Full details and data files)

Version 1.0: 2014-04-16
Type: Initial release
Version 1.1: 2014-05-14
Changes: Database references
Version 1.2: 2017-08-02
Changes: Refinement description, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-27
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

4O58 | pdb_00004o58

Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/3/1975 (H3N2) influenza hemagglutinin

Literature

Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Expand

Oligosaccharides

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)