7JZK | pdb_00007jzk

Crystal structure of LAIR1 ectodomain (from MGD21) in complex with Plasmodium RIFIN (PF3D7_0401300) V2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.275 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural basis of LAIR1 targeting by polymorphic Plasmodium RIFINs.

Xu, K.Wang, Y.Shen, C.H.Chen, Y.Zhang, B.Liu, K.Tsybovsky, Y.Wang, S.Farney, S.K.Gorman, J.Stephens, T.Verardi, R.Yang, Y.Zhou, T.Chuang, G.Y.Lanzavecchia, A.Piccoli, L.Kwong, P.D.

(2021) Nat Commun 12: 4226-4226

  • DOI: https://doi.org/10.1038/s41467-021-24291-6
  • Primary Citation Related Structures: 
    7JZ1, 7JZ4, 7JZI, 7JZK

  • PubMed Abstract: 

    RIFIN, a large family of Plasmodium variant surface antigens, plays a crucial role in malaria pathogenesis by mediating immune suppression through activation of inhibitory receptors such as LAIR1, and antibodies with LAIR1 inserts have been identified that bind infected erythrocytes through RIFIN. However, details of RIFIN-mediated LAIR1 recognition and receptor activation have been unclear. Here, we use negative-stain EM to define the architecture of LAIR1-inserted antibodies and determine crystal structures of RIFIN-variable 2 (V2) domain in complex with a LAIR1 domain. These structures reveal the LAIR1-binding region of RIFIN to be hydrophobic and membrane-distal, to exhibit extensive structural diversity, and to interact with RIFIN-V2 in a one-to-one fashion. Through structural and sequence analysis of various LAIR1 constructs, we identify essential elements of RIFIN-binding on LAIR1. Furthermore, a structure-derived LAIR1-binding sequence signature ascertained >20 LAIR1-binding RIFINs, including some from P. falciparum field strains and Plasmodium species infecting gorillas and chimpanzees.


  • Organizational Affiliation
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. xu.4692@osu.edu.

Macromolecule Content 

  • Total Structure Weight: 55.74 kDa 
  • Atom Count: 3,468 
  • Modeled Residue Count: 442 
  • Deposited Residue Count: 512 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LAIR1 ecotodomain from MGD21 antibodyA [auth C],
C [auth A]
105Homo sapiensMutation(s): 0 
UniProt
Find proteins for A0A6B9UEV8 (Homo sapiens)
Explore A0A6B9UEV8 
Go to UniProtKB:  A0A6B9UEV8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6B9UEV8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
RifinB [auth D],
D [auth B]
151Plasmodium falciparum NF54Mutation(s): 0 
Gene Names: CK202_1428PFNF54_00613
UniProt
Find proteins for Q8I211 (Plasmodium falciparum (isolate 3D7))
Explore Q8I211 
Go to UniProtKB:  Q8I211
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I211
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.275 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.118α = 90
b = 95.839β = 103.97
c = 71.828γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary