6NZ7

Crystal structure of broadly neutralizing Influenza A antibody 429 B01 in complex with Hemagglutinin Hong Kong 1968


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Prolonged evolution of the memory B cell response induced by a replicating adenovirus-influenza H5 vaccine.

Matsuda, K.Huang, J.Zhou, T.Sheng, Z.Kang, B.H.Ishida, E.Griesman, T.Stuccio, S.Bolkhovitinov, L.Wohlbold, T.J.Chromikova, V.Cagigi, A.Leung, K.Andrews, S.Cheung, C.S.F.Pullano, A.A.Plyler, J.Soto, C.Zhang, B.Yang, Y.Joyce, M.G.Tsybovsky, Y.Wheatley, A.Narpala, S.R.Guo, Y.Darko, S.Bailer, R.T.Poole, A.Liang, C.J.Smith, J.Alexander, J.Gurwith, M.Migueles, S.A.Koup, R.A.Golding, H.Khurana, S.McDermott, A.B.Shapiro, L.Krammer, F.Kwong, P.D.Connors, M.

(2019) Sci Immunol 4

  • DOI: https://doi.org/10.1126/sciimmunol.aau2710
  • Primary Citation of Related Structures:  
    6NZ7

  • PubMed Abstract: 

    Induction of an antibody response capable of recognizing highly diverse strains is a major obstacle to the development of vaccines for viruses such as HIV and influenza. Here, we report the dynamics of B cell expansion and evolution at the single-cell level after vaccination with a replication-competent adenovirus type 4 recombinant virus expressing influenza H5 hemagglutinin. Fluorescent H1 or H5 probes were used to quantitate and isolate peripheral blood B cells and their antigen receptors. We observed increases in H5-specific antibody somatic hypermutation and potency for several months beyond the period of active viral replication that was not detectable at the serum level. Individual broad and potent antibodies could be isolated, including one stem-specific antibody that is part of a new multidonor class. These results demonstrate prolonged evolution of the B cell response for months after vaccination and should be considered in efforts to evaluate or boost vaccine-induced immunity.


  • Organizational Affiliation

    HIV-Specific Immunity Section of the Laboratory of Immunoregulation, National Institutes of Health (NIH), Bethesda, MD 20892, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, E
319Influenza 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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91MA7
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, F
173Influenza 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  
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UniProt GroupQ91MA7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
429 B01 FAB heavy chainC [auth H],
G
228Homo sapiensMutation(s): 0 
UniProt
Find proteins for A8K008 (Homo sapiens)
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UniProt GroupA8K008
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
429 B01 FAB light chainD [auth L],
H [auth I]
214Homo sapiensMutation(s): 0 
UniProt
Find proteins for Q8TCD0 (Homo sapiens)
Explore Q8TCD0 
Go to UniProtKB:  Q8TCD0
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UniProt GroupQ8TCD0
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth B],
N [auth H],
O [auth E],
P [auth E],
Q [auth E],
R [auth F],
S [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.769α = 90
b = 123.905β = 112
c = 119.338γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary