6UTA

Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for Zika envelope domain III recognition by a germline version of a recurrent neutralizing antibody.

Esswein, S.R.Gristick, H.B.Jurado, A.Peace, A.Keeffe, J.R.Lee, Y.E.Voll, A.V.Saeed, M.Nussenzweig, M.C.Rice, C.M.Robbiani, D.F.MacDonald, M.R.Bjorkman, P.J.

(2020) Proc Natl Acad Sci U S A 117: 9865-9875

  • DOI: 10.1073/pnas.1919269117
  • Primary Citation of Related Structures:  
    6UTE, 6UTA

  • PubMed Abstract: 
  • Recent epidemics demonstrate the global threat of Zika virus (ZIKV), a flavivirus transmitted by mosquitoes. Although infection is usually asymptomatic or mild, newborns of infected mothers can display severe symptoms, including neurodevelopmental abnormalities and microcephaly ...

    Recent epidemics demonstrate the global threat of Zika virus (ZIKV), a flavivirus transmitted by mosquitoes. Although infection is usually asymptomatic or mild, newborns of infected mothers can display severe symptoms, including neurodevelopmental abnormalities and microcephaly. Given the large-scale spread, symptom severity, and lack of treatment or prophylaxis, a safe and effective ZIKV vaccine is urgently needed. However, vaccine design is complicated by concern that elicited antibodies (Abs) may cross-react with other flaviviruses that share a similar envelope protein, such as dengue virus, West Nile virus, and yellow fever virus. This cross-reactivity may worsen symptoms of a subsequent infection through Ab-dependent enhancement. To better understand the neutralizing Ab response and risk of Ab-dependent enhancement, further information on germline Ab binding to ZIKV and the maturation process that gives rise to potently neutralizing Abs is needed. Here we use binding and structural studies to compare mature and inferred-germline Ab binding to envelope protein domain III of ZIKV and other flaviviruses. We show that affinity maturation of the light-chain variable domain is important for strong binding of the recurrent VH3-23/VK1-5 neutralizing Abs to ZIKV envelope protein domain III, and identify interacting residues that contribute to weak, cross-reactive binding to West Nile virus. These findings provide insight into the affinity maturation process and potential cross-reactivity of VH3-23/VK1-5 neutralizing Abs, informing precautions for protein-based vaccines designed to elicit germline versions of neutralizing Abs.


    Organizational Affiliation

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125; bjorkman@caltech.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Z004 iGL Fab heavy chainD [auth A], A [auth H]234Homo sapiensMutation(s): 0 
UniProt
Find proteins for S6C4S0 (Homo sapiens)
Explore S6C4S0 
Go to UniProtKB:  S6C4S0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Z004 iGL Fab light chainE [auth B], B [auth L]214Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX7 (Homo sapiens)
Explore P0DOX7 
Go to UniProtKB:  P0DOX7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
EnvF [auth C], C [auth E]110Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013Mutation(s): 0 
EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt)
UniProt
Find proteins for A0A142I5B9 (Zika virus (isolate ZIKV/Human/Cambodia/FSS13025/2010))
Explore A0A142I5B9 
Go to UniProtKB:  A0A142I5B9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.907α = 90
b = 85.907β = 90
c = 327.458γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesP01-1-ROCKU.AI138938
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32-GM007616-40
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesF30AI147579
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32-GM008042

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-15
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2020-05-20
    Changes: Database references