6MN7 | pdb_00006mn7

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6MN7

This is version 2.1 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: https://doi.org/10.1038/s41467-019-09481-7
  • Primary Citation Related Structures: 
    6MN7

  • 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 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
    • Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.

Macromolecule Content 

  • Total Structure Weight: 325.97 kDa 
  • Atom Count: 21,447 
  • Modeled Residue Count: 2,418 
  • Deposited Residue Count: 2,595 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope Glycoprotein gp120
A, C, D
476Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1)
Explore Q2N0S6 
Go to UniProtKB:  Q2N0S6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S6
Glycosylation
Glycosylation Sites: 14
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope Glycoprotein gp41
B, E, F
153Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus type 1)
Explore Q2N0S7 
Go to UniProtKB:  Q2N0S7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2N0S7
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
BF520.1 Fab variable region
G, H, I
236Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseGA [auth g],
P,
WA [auth w]
7N/A
Glycosylation Resources
GlyTouCan: G07617FP
GlyCosmos: G07617FP
GlyGen: G07617FP
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseIA [auth i],
R,
YA [auth y]
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJA [auth j],
S,
ZA [auth z]
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL
GlyCosmos: G55220VL
GlyGen: G55220VL
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAB [auth 0],
KA [auth k],
T
10N/A
Glycosylation Resources
GlyTouCan: G40702WU
GlyCosmos: G40702WU
GlyGen: G40702WU

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
IB [auth A]
JB [auth B]
KB [auth B]
LB [auth C]
MB [auth D]
IB [auth A],
JB [auth B],
KB [auth B],
LB [auth C],
MB [auth D],
NB [auth E],
OB [auth E],
PB [auth F],
QB [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: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary