4O58

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
R-Value Work: 0.177
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

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

Macromolecules

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03435
Sequence Annotations Expand
Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03435
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Reference Sequence

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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
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Reference Sequence

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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S6C4S0
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Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	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	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 O [auth B] SDF format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A]	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]	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 I [auth A] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain S [auth L] SDF format, chain X [auth H] SDF format, chain Y [auth H] 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 Q [auth B] SDF format, chain T [auth L] SDF format, chain W [auth H] SDF format, chain Z [auth H] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth L] MOL2 format, chain X [auth H] MOL2 format, chain Y [auth H] 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 Q [auth B] MOL2 format, chain T [auth L] MOL2 format, chain W [auth H] MOL2 format, chain Z [auth H]	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
R-Value Work: 0.177
R-Value Observed: 0.180
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

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

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Help and Resources

4O58

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

Entity Groups

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Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)