7N65 | pdb_00007n65

Complex structure of HIV superinfection Fab QA013.2 and BG505.SOSIP.664


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7N65

This is version 1.1 of the entry. See complete history

Literature

Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection.

Shipley, M.M.Mangala Prasad, V.Doepker, L.E.Dingens, A.S.Ralph, D.K.Harkins, E.Dhar, A.Arenz, D.Chohan, V.Weight, H.Mandaliya, K.Bloom, J.D.Matsen Iv, F.Lee, K.K.Overbaugh, J.M.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.68110
  • Primary Citation Related Structures: 
    7N65

  • PubMed Abstract: 

    Stimulating broadly neutralizing antibodies (bnAbs) directly from germline remains a barrier for HIV vaccines. HIV superinfection elicits bnAbs more frequently than single infection, providing clues of how to elicit such responses. We used longitudinal antibody sequencing and structural studies to characterize bnAb development from a superinfection case. BnAb QA013.2 bound initial and superinfecting viral Env, despite its probable naive progenitor only recognizing the superinfecting strain, suggesting both viruses influenced this lineage. A 4.15 Å cryo-EM structure of QA013.2 bound to native-like trimer showed recognition of V3 signatures (N301/N332 and GDIR). QA013.2 relies less on CDRH3 and more on framework and CDRH1 for affinity and breadth compared to other V3/glycan-specific bnAbs. Antigenic profiling revealed that viral escape was achieved by changes in the structurally-defined epitope and by mutations in V1. These results highlight shared and novel properties of QA013.2 relative to other V3/glycan-specific bnAbs in the setting of sequential, diverse antigens.


  • Organizational Affiliation
    • Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, United States.

Macromolecule Content 

  • Total Structure Weight: 338.33 kDa 
  • Atom Count: 21,525 
  • Modeled Residue Count: 2,454 
  • Deposited Residue Count: 2,715 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41
A, E, I
508Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: env
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp41
B, F, J
161Human immunodeficiency virus 1Mutation(s): 0 
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab QA013.2 Heavy Chain, variable region
C, G, K
128Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab QA013.2 Light Chain, , variable region
D, H, L
108Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 7
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-glucopyranoseAB [auth 0],
JA [auth j],
S
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G07617FP
GlyCosmos: G07617FP
GlyGen: G07617FP
Entity ID: 8
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-glucopyranoseCB [auth 2],
LA [auth l],
U
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 9
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-glucopyranoseDB [auth 3],
MA [auth m],
V
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL
GlyCosmos: G55220VL
GlyGen: G55220VL
Entity ID: 10
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)]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-glucopyranoseEB [auth 4],
NA [auth n],
W
8N-Glycosylation
Glycosylation Resources
GlyTouCan: G80966KZ
GlyCosmos: G80966KZ
GlyGen: G80966KZ

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
LB [auth A]
MB [auth B]
NB [auth B]
PB [auth E]
QB [auth F]
LB [auth A],
MB [auth B],
NB [auth B],
PB [auth E],
QB [auth F],
RB [auth F],
TB [auth I],
UB [auth J],
VB [auth J]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN

Query on MAN



Download:Ideal Coordinates CCD File
OB [auth C],
SB [auth G],
WB [auth K]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI138709

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary