5IGX

Crystal structure of NIH45-46 Fab germline precursor in complex with 426c.TM1deltaV1-3 gp120


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural basis for germline antibody recognition of HIV-1 immunogens.

Scharf, L.West, A.P.Sievers, S.A.Chen, C.Jiang, S.Gao, H.Gray, M.D.McGuire, A.T.Scheid, J.F.Nussenzweig, M.C.Stamatatos, L.Bjorkman, P.J.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.13783
  • Primary Citation of Related Structures:  
    5F7E, 5FA2, 5FEC, 5I9Q, 5IGX

  • PubMed Abstract: 

    Efforts to elicit broadly neutralizing antibodies (bNAbs) against HIV-1 require understanding germline bNAb recognition of HIV-1 envelope glycoprotein (Env). The VRC01-class bNAb family derived from the VH1-2*02 germline allele arose in multiple HIV-1-infected donors, yet targets the CD4-binding site on Env with common interactions. Modified forms of the 426c Env that activate germline-reverted B cell receptors are candidate immunogens for eliciting VRC01-class bNAbs. We present structures of germline-reverted VRC01-class bNAbs alone and complexed with 426c-based gp120 immunogens. Germline bNAb-426c gp120 complexes showed preservation of VRC01-class signature residues and gp120 contacts, but detectably different binding modes compared to mature bNAb-gp120 complexes. Unlike typical antibody-antigen interactions, VRC01-class germline antibodies exhibited preformed antigen-binding conformations for recognizing immunogens. Affinity maturation introduced substitutions increasing induced-fit recognition and electropositivity, potentially to accommodate negatively-charged complex-type N-glycans on gp120. These results provide general principles relevant to the unusual evolution of VRC01-class bNAbs and guidelines for structure-based immunogen design.


  • Organizational Affiliation

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
426c.TM1deltaV1-3 gp120A [auth G]353Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for A0A0K1H6P9 (Human immunodeficiency virus 1)
Explore A0A0K1H6P9 
Go to UniProtKB:  A0A0K1H6P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K1H6P9
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
germline NIH45-46 Fab heavy chainB [auth H]236Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
germline NIH45-46 light chainC [auth L]210Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.39 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.284α = 90
b = 168.533β = 90
c = 176.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI100148
Bill & Melinda Gates FoundationUnited States1040753
American Cancer SocietyUnited StatesPF-13-076-01-MPC

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Advisory, Author supporting evidence, Derived calculations
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary