6WXL | pdb_00006wxl

Cryo-EM structure of the VRC315 clinical trial, vaccine-elicited, human antibody 1D12 in complex with an H7 SH13 HA trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure of an influenza group 2-neutralizing antibody targeting the hemagglutinin stem supersite.

Cheung, C.S.Gorman, J.Andrews, S.F.Rawi, R.Reveiz, M.Shen, C.H.Wang, Y.Harris, D.R.Nazzari, A.F.Olia, A.S.Raab, J.Teng, I.T.Verardi, R.Wang, S.Yang, Y.Chuang, G.Y.McDermott, A.B.Zhou, T.Kwong, P.D.

(2022) Structure 

  • DOI: https://doi.org/10.1016/j.str.2022.04.003
  • Primary Citation Related Structures: 
    6WXL

  • PubMed Abstract: 

    Several influenza antibodies with broad group 2 neutralization have recently been isolated. Here, we analyze the structure, class, and binding of one of these antibodies from an H7N9 vaccine trial, 315-19-1D12. The cryo-EM structure of 315-19-1D12 Fab in complex with the hemagglutinin (HA) trimer revealed the antibody to recognize the helix A region of the HA stem, at the supersite of vulnerability recognized by group 1-specific and by cross-group-neutralizing antibodies. 315-19-1D12 was derived from HV1-2 and KV2-28 genes and appeared to form a new antibody class. Bioinformatic analysis indicated its group 2 neutralization specificity to be a consequence of four key residue positions. We specifically tested the impact of the group 1-specific N33 glycan, which decreased but did not abolish group 2 binding of 315-19-1D12. Overall, this study highlights the recognition of a broad group 2-neutralizing antibody, revealing unexpected diversity in neutralization specificity for antibodies that recognize the HA stem supersite.


  • Organizational Affiliation
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content 

  • Total Structure Weight: 329.85 kDa 
  • Atom Count: 17,016 
  • Modeled Residue Count: 2,175 
  • Deposited Residue Count: 2,985 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chainA,
K [auth C],
L [auth G]
321Influenza A virus (A/Shanghai/JS01/2013(H7N9))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A067Y6L0 (Influenza A virus)
Explore A0A067Y6L0 
Go to UniProtKB:  A0A067Y6L0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A067Y6L0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chainB,
E [auth D],
H [auth I]
221Influenza A virus (A/Shanghai/JS01/2013(H7N9))Mutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A067Y6L0 (Influenza A virus)
Explore A0A067Y6L0 
Go to UniProtKB:  A0A067Y6L0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A067Y6L0
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
1D12 Light chainC [auth L],
F [auth E],
I [auth J]
221Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
1D21 Heavy chainD [auth H],
G [auth F],
J [auth K]
232Homo sapiensMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
M [auth A]
N [auth B]
O [auth B]
P [auth D]
Q [auth D]
M [auth A],
N [auth B],
O [auth B],
P [auth D],
Q [auth D],
R [auth I],
S [auth I],
T [auth C],
U [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.12
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2022-06-22
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Refinement description, Structure summary