6Q23

Crystal structure of human 1G01 Fab in complex with influenza virus neuraminidase from A/California/04/2009 (H1N1)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


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


Literature

Broadly protective human antibodies that target the active site of influenza virus neuraminidase.

Stadlbauer, D., Zhu, X., McMahon, M., Turner, J.S., Wohlbold, T.J., Schmitz, A.J., Strohmeier, S., Yu, W., Nachbagauer, R., Mudd, P.A., Wilson, I.A., Ellebedy, A.H., Krammer, F.

(2019) Science 366: 499-504

  • DOI: https://doi.org/10.1126/science.aay0678
  • Primary Citation of Related Structures:  
    6Q1Z, 6Q20, 6Q23

  • PubMed Abstract: 

    Better vaccines against influenza virus are urgently needed to provide broader protection against diverse strains, subtypes, and types. Such efforts are assisted by the identification of novel broadly neutralizing epitopes targeted by protective antibodies. Influenza vaccine development has largely focused on the hemagglutinin, but the other major surface antigen, the neuraminidase, has reemerged as a potential target for universal vaccines. We describe three human monoclonal antibodies isolated from an H3N2-infected donor that bind with exceptional breadth to multiple different influenza A and B virus neuraminidases. These antibodies neutralize the virus, mediate effector functions, are broadly protective in vivo, and inhibit neuraminidase activity by directly binding to the active site. Structural and functional characterization of these antibodies will inform the development of neuraminidase-based universal vaccines against influenza virus.

    • Organizational Affiliation: 

    Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NeuraminidaseA [auth C],
B,
C [auth A],
D		391Influenza A virus (A/California/04/2009(H1N1))Mutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for C3W5S3 (Influenza A virus (strain swl A/California/04/2009 H1N1))
Explore C3W5S3 
Go to UniProtKB:  C3W5S3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3W5S3
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
1G01 Fab IgG1 heavy chainE [auth H],
G [auth E],
I [auth G],
K [auth J]		240Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
1G01 Fab kappa light chainF [auth L],
H [auth F],
J [auth I],
L [auth K]		216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AA [auth D]
M [auth C]
P [auth C]
Q [auth B]
T [auth B]
AA [auth D],
M [auth C],
P [auth C],
Q [auth B],
T [auth B],
U [auth A],
V [auth A],
Y [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA (Subject of Investigation/LOI)
Query on CA
Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
N [auth C]
O [auth C]
R [auth B]
BA [auth D],
CA [auth D],
N [auth C],
O [auth C],
R [auth B],
S [auth B],
W [auth A],
X [auth A],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.594α = 90
b = 234.985β = 106.4
c = 106.275γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI117675-01

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    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: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-10-30
    Changes: Structure summary