6CNV

INFLUENZA B/BRISBANE HEMAGGLUTININ FAB CR9115 SD84H COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin.

Laursen, N.S.Friesen, R.H.E.Zhu, X.Jongeneelen, M.Blokland, S.Vermond, J.van Eijgen, A.Tang, C.van Diepen, H.Obmolova, G.van der Neut Kolfschoten, M.Zuijdgeest, D.Straetemans, R.Hoffman, R.M.B.Nieusma, T.Pallesen, J.Turner, H.L.Bernard, S.M.Ward, A.B.Luo, J.Poon, L.L.M.Tretiakova, A.P.Wilson, J.M.Limberis, M.P.Vogels, R.Brandenburg, B.Kolkman, J.A.Wilson, I.A.

(2018) Science 362: 598-602

  • DOI: 10.1126/science.aaq0620
  • Primary Citation of Related Structures:  
    6CK8, 6CNV, 6CNW, 6FYS, 6FYT, 6FYU, 6FYW

  • PubMed Abstract: 
  • Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency ...

    Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens.


    Organizational Affiliation

    Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HemagglutininA347Influenza B virus (B/Townsville/202/2008)Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for U3RVK6 (Influenza B virus)
Explore U3RVK6 
Go to UniProtKB:  U3RVK6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope glycoproteinB220Influenza B virus (B/Townsville/202/2008)Human immunodeficiency virus 1
This entity is chimeric
Mutation(s): 0 
UniProt
Find proteins for C0LT38 (Influenza B virus)
Explore C0LT38 
Go to UniProtKB:  C0LT38
Find proteins for P10104 (Enterobacteria phage T4)
Explore P10104 
Go to UniProtKB:  P10104
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SD84hC116synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CR9114 Light chainD [auth L]216Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
CR9114 Fab heavy chainE [auth H]230Homo sapiensMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth D], G [auth E], H [auth F], I [auth G]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
J [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.78α = 90
b = 190.78β = 90
c = 190.78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2018-03-09 
  • Released Date: 2018-11-14 
  • Deposition Author(s): Luo, J., Obmolova, G.

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary