7T17 | pdb_00007t17

Zika Virus asymmetric unit bound with IgM antibody DH1017 Fab fragment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7T17

This is version 1.4 of the entry. See complete history

Literature

A Zika virus-specific IgM elicited in pregnancy exhibits ultrapotent neutralization.

Singh, T.Hwang, K.K.Miller, A.S.Jones, R.L.Lopez, C.A.Dulson, S.J.Giuberti, C.Gladden, M.A.Miller, I.Webster, H.S.Eudailey, J.A.Luo, K.Von Holle, T.Edwards, R.J.Valencia, S.Burgomaster, K.E.Zhang, S.Mangold, J.F.Tu, J.J.Dennis, M.Alam, S.M.Premkumar, L.Dietze, R.Pierson, T.C.Ooi, E.E.Lazear, H.M.Kuhn, R.J.Permar, S.R.Bonsignori, M.

(2022) Cell 185: 4826-4840.e17

  • DOI: https://doi.org/10.1016/j.cell.2022.10.023
  • Primary Citation Related Structures: 
    7T17

  • PubMed Abstract: 

    Congenital Zika virus (ZIKV) infection results in neurodevelopmental deficits in up to 14% of infants born to ZIKV-infected mothers. Neutralizing antibodies are a critical component of protective immunity. Here, we demonstrate that plasma IgM contributes to ZIKV immunity in pregnancy, mediating neutralization up to 3 months post-symptoms. From a ZIKV-infected pregnant woman, we isolated a pentameric ZIKV-specific IgM (DH1017.IgM) that exhibited ultrapotent ZIKV neutralization dependent on the IgM isotype. DH1017.IgM targets an envelope dimer epitope within domain II. The epitope arrangement on the virion is compatible with concurrent engagement of all ten antigen-binding sites of DH1017.IgM, a solution not available to IgG. DH1017.IgM protected mice against viremia upon lethal ZIKV challenge more efficiently than when expressed as an IgG. Our findings identify a role for antibodies of the IgM isotype in protection against ZIKV and posit DH1017.IgM as a safe and effective candidate immunotherapeutic, particularly during pregnancy.


  • Organizational Affiliation
    • Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA; Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94709, USA.

Macromolecule Content 

  • Total Structure Weight: 199.68 kDa 
  • Atom Count: 7,412 
  • Modeled Residue Count: 1,853 
  • Deposited Residue Count: 1,853 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DH1017.IgM FabC constant domainA [auth H]105Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
Explore P0DOX5 
Go to UniProtKB:  P0DOX5
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UniProt GroupP0DOX5
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DH1017.IgM LambdaC constant domainB [auth I]106Homo sapiensMutation(s): 0 
Gene Names: IGLL5
UniProt
Find proteins for B9A064 (Homo sapiens)
Explore B9A064 
Go to UniProtKB:  B9A064
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UniProt GroupB9A064
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DH1017.IgM IgHC [auth J],
E [auth F]
123Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DH1017.IgM IgLD [auth K],
F [auth G]
110Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Core proteinG [auth A],
H [auth C],
I [auth E]
392Zika virusMutation(s): 0 
EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
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UniProt GroupA0A024B7W1
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2022-11-30
    Changes: Database references
  • Version 1.2: 2022-12-21
    Changes: Database references
  • Version 1.3: 2024-06-05
    Changes: Data collection, Refinement description
  • Version 1.4: 2026-04-22
    Changes: Data collection, Other, Structure summary