6MN7

Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 antigen binding fragment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage.

Simonich, C.A.Doepker, L.Ralph, D.Williams, J.A.Dhar, A.Yaffe, Z.Gentles, L.Small, C.T.Oliver, B.Vigdorovich, V.Mangala Prasad, V.Nduati, R.Sather, D.N.Lee, K.K.Matsen Iv, F.A.Overbaugh, J.

(2019) Nat Commun 10: 2190-2190

  • DOI: 10.1038/s41467-019-09481-7

  • PubMed Abstract: 
  • HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine targets. Here we reconstruct the developmental linea ...

    HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine targets. Here we reconstruct the developmental lineage of BF520.1, an infant-derived HIV-specific broadly neutralizing antibody (bnAb), using computational methods developed specifically for this purpose. We find that the BF520.1 inferred naive precursor binds HIV Env. We also show that heterologous cross-clade neutralizing activity evolved in the infant within six months of infection and that, ultimately, only 2% SHM is needed to achieve the full breadth of the mature antibody. Mutagenesis and structural analyses reveal that, for this infant bnAb, substitutions in the kappa chain were critical for activity, particularly in CDRL1. Overall, the developmental pathway of this infant antibody includes features distinct from adult antibodies, including several that may be amenable to better vaccine responses.


    Organizational Affiliation

    Department of Pediatrics and Child Health, University of Nairobi, Nairobi, Kenya.,Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA, 98195, USA.,Department of Medicinal Chemistry, University of Washington, Seattle, WA, 98195, USA.,Department of Statistics, University of Washington, Seattle, WA, 98195, USA.,Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.,Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA, 98195, USA. joverbau@fredhutch.org.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.,Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.,Center for Infectious Disease Research, Seattle, WA, 98109, USA.,Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA. joverbau@fredhutch.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Envelope Glycoprotein gp120
A, C, D
476Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
Find proteins for Q2N0S6 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Envelope Glycoprotein gp41
B, E, F
153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
Find proteins for Q2N0S7 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q2N0S7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BF520.1 Fab variable region
G, H, I
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, C, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, C, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-06-05
    Type: Data collection, Database references