8UT5 | pdb_00008ut5

CryoEM structure of A/Michigan/45/2015 H1 in complex with flu HA central stem VH1-18 antibody UCA6_N55T


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8UT5

This is version 1.2 of the entry. See complete history

Literature

Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses.

Ray, R.Nait Mohamed, F.A.Maurer, D.P.Huang, J.Alpay, B.A.Ronsard, L.Xie, Z.Han, J.Fernandez-Quintero, M.Phan, Q.A.Ursin, R.L.Vu, M.Kirsch, K.H.Prum, T.Rosado, V.C.Bracamonte-Moreno, T.Okonkwo, V.Bals, J.McCarthy, C.Nair, U.Kanekiyo, M.Ward, A.B.Schmidt, A.G.Batista, F.D.Lingwood, D.

(2024) Immunity 57: 1141-1159.e11

  • DOI: https://doi.org/10.1016/j.immuni.2024.03.022
  • Primary Citation Related Structures: 
    8UT3, 8UT4, 8UT5, 8UT6, 8UT7, 8UT8, 8UT9, 8UWA

  • PubMed Abstract: 

    Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.


  • Organizational Affiliation
    • The Ragon Institute of Mass General, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.

Macromolecule Content 

  • Total Structure Weight: 222.65 kDa 
  • Atom Count: 13,615 
  • Modeled Residue Count: 1,693 
  • Deposited Residue Count: 1,958 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA1 chain
A, C, E
324Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A1J0CXU0 (Influenza A virus)
Explore A0A1J0CXU0 
Go to UniProtKB:  A0A1J0CXU0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1J0CXU0
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hemagglutinin HA2 chain
B, D, F
250Influenza A virusMutation(s): 0 
Gene Names: HA
UniProt
Find proteins for A0A109YUH3 (Influenza A virus)
Explore A0A109YUH3 
Go to UniProtKB:  A0A109YUH3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A109YUH3
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
UCA6_N55T HC Fv127Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
UCA6_N55T LC Fv109Homo sapiensMutation(s): 0 

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth C],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth D],
T [auth E],
U [auth E],
V [auth E],
W [auth E],
X [auth E],
Y [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesINV-004923

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Structure summary