8SAL | pdb_00008sal

CryoEM structure of VRC01-CH848.0358.80


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8SAL

This is version 1.3 of the entry. See complete history

Literature

Structural basis for breadth development in the HIV-1 V3-glycan targeting DH270 antibody clonal lineage.

Henderson, R.Zhou, Y.Stalls, V.Wiehe, K.Saunders, K.O.Wagh, K.Anasti, K.Barr, M.Parks, R.Alam, S.M.Korber, B.Haynes, B.F.Bartesaghi, A.Acharya, P.

(2023) Nat Commun 14: 2782-2782

  • DOI: https://doi.org/10.1038/s41467-023-38108-1
  • Primary Citation Related Structures: 
    8SAL, 8SAN, 8SAQ, 8SAR, 8SAS, 8SAT, 8SAU, 8SAV, 8SAW, 8SAX, 8SAY, 8SAZ, 8SB0, 8SB1, 8SB2, 8SB3, 8SB4, 8SB5

  • PubMed Abstract: 

    Antibody affinity maturation enables adaptive immune responses to a wide range of pathogens. In some individuals broadly neutralizing antibodies develop to recognize rapidly mutating pathogens with extensive sequence diversity. Vaccine design for pathogens such as HIV-1 and influenza has therefore focused on recapitulating the natural affinity maturation process. Here, we determine structures of antibodies in complex with HIV-1 Envelope for all observed members and ancestral states of the broadly neutralizing HIV-1 V3-glycan targeting DH270 antibody clonal B cell lineage. These structures track the development of neutralization breadth from the unmutated common ancestor and define affinity maturation at high spatial resolution. By elucidating contacts mediated by key mutations at different stages of antibody development we identified sites on the epitope-paratope interface that are the focus of affinity optimization. Thus, our results identify bottlenecks on the path to natural affinity maturation and reveal solutions for these that will inform immunogen design aimed at eliciting a broadly neutralizing immune response by vaccination.


  • Organizational Affiliation
    • Department of Medicine and Immunology, Duke University School of Medicine, Durham, NC, USA. rory.henderson@duke.edu.

Macromolecule Content 

  • Total Structure Weight: 286.9 kDa 
  • Atom Count: 18,435 
  • Modeled Residue Count: 2,343 
  • Deposited Residue Count: 2,556 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CH0848.3.D0358.80.06CHIM.DS.6R.SOSIP gp120
A, E, I
475HIV-1 06TG.HT008Mutation(s): 0 
UniProt
Find proteins for A0A1W6IG54 (Human immunodeficiency virus type 1)
Explore A0A1W6IG54 
Go to UniProtKB:  A0A1W6IG54
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1W6IG54
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CH0848.3.D0358.80.06CHIM.DS.6R.SOSIP gp41
B, F, J
153HIV-1 06TG.HT008Mutation(s): 0 
UniProt
Find proteins for A0ACD6BAD8 (Simian-Human immunodeficiency virus)
Explore A0ACD6BAD8 
Go to UniProtKB:  A0ACD6BAD8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6BAD8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
VCR01 variable heavy chain
C, G, K
121Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
VCR01 variable light chain
D, H, L
103Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesECCS-2025064
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI144371
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI145687

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-19
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-05-21
    Changes: Data collection