5UMN | pdb_00005umn

Crystal structure of C05 VPGSGW mutant bound to H3 influenza hemagglutinin, HA1 subunit

PDB DOI: https://doi.org/10.2210/pdb5UMN/pdb

Classification: IMMUNE SYSTEM
Organism(s): Influenza A virus (A/Hong Kong/1/1968(H3N2)), Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2017-01-27 Released: 2017-05-24
Deposition Author(s): Wu, N.C., Wilson, I.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.208 (Depositor), 0.215 (DCC)
R-Value Work:
0.181 (Depositor), 0.189 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity.

Wu, N.C., Grande, G., Turner, H.L., Ward, A.B., Xie, J., Lerner, R.A., Wilson, I.A.

(2017) Nat Commun 8: 15371-15371

PubMed: 28504265 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/ncomms15371
Primary Citation Related Structures:
5UMN

PubMed Abstract:
The relatively recent discovery and characterization of human broadly neutralizing antibodies (bnAbs) against influenza virus provide valuable insights into antiviral and vaccine development. However, the factors that influence the evolution of high-affinity bnAbs remain elusive. We therefore explore the functional sequence space of bnAb C05, which targets the receptor-binding site (RBS) of influenza haemagglutinin (HA) via a long CDR H3. We combine saturation mutagenesis with yeast display to enrich for C05 variants of CDR H3 that bind to H1 and H3 HAs. The C05 variants evolve up to 20-fold higher affinity but increase specificity to each HA subtype used in the selection. Structural analysis reveals that the fine specificity is strongly influenced by a highly conserved substitution that regulates receptor binding in different subtypes. Overall, this study suggests that subtle natural variations in the HA RBS between subtypes and species may differentially influence the evolution of high-affinity bnAbs.

Organizational Affiliation

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA.

Macromolecule Content

Total Structure Weight: 162.36 kDa
Atom Count: 12,093
Modeled Residue Count: 1,412
Deposited Residue Count: 1,470
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin	A, B	274	Influenza A virus (A/Hong Kong/1/1968(H3N2))	Mutation(s): 0 Gene Names: HA
UniProt
Find proteins for Q91MA7 (Influenza A virus (strain A/Hong Kong/1/1968 H3N2)) Explore Q91MA7 Go to UniProtKB: Q91MA7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q91MA7
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody C05 VPGSGW mutant, heavy chain	C, E	247	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody C05, light chain	D, F	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	I [auth A], L [auth B], M [auth B], N [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth A], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C]	P [auth C], Q [auth C]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain P [auth C] Focus chain Q [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Interactions & Density Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.208 (Depositor), 0.215 (DCC)
R-Value Work: 0.181 (Depositor), 0.189 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.344	α = 90
b = 88.344	β = 90
c = 255.038	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-05-24

Deposition Author(s):

Wu, N.C.

Wilson, I.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R56 AI117675

Revision History (Full details and data files)

Version 1.0: 2017-05-24
Type: Initial release
Version 1.1: 2017-05-31
Changes: Database references
Version 1.2: 2017-09-06
Changes: Author supporting evidence
Version 1.3: 2019-12-11
Changes: Author supporting evidence
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.6: 2024-10-16
Changes: Structure summary