Human receptor NKR-P1 in deglycosylated form, extracellular domain

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.

Blaha, J.Skalova, T.Kalouskova, B.Skorepa, O.Cmunt, D.Grobarova, V.Pazicky, S.Polachova, E.Abreu, C.Stransky, J.Koval, T.Duskova, J.Zhao, Y.Harlos, K.Hasek, J.Dohnalek, J.Vanek, O.

(2022) Nat Commun 13: 5022-5022

  • DOI: https://doi.org/10.1038/s41467-022-32577-6
  • Primary Citation of Related Structures:  
    5MGR, 5MGS, 5MGT

  • PubMed Abstract: 

    Signaling by the human C-type lectin-like receptor, natural killer (NK) cell inhibitory receptor NKR-P1, has a critical role in many immune-related diseases and cancer. C-type lectin-like receptors have weak affinities to their ligands; therefore, setting up a comprehensive model of NKR-P1-LLT1 interactions that considers the natural state of the receptor on the cell surface is necessary to understand its functions. Here we report the crystal structures of the NKR-P1 and NKR-P1:LLT1 complexes, which provides evidence that NKR-P1 forms homodimers in an unexpected arrangement to enable LLT1 binding in two modes, bridging two LLT1 molecules. These interaction clusters are suggestive of an inhibitory immune synapse. By observing the formation of these clusters in solution using SEC-SAXS analysis, by dSTORM super-resolution microscopy on the cell surface, and by following their role in receptor signaling with freshly isolated NK cells, we show that only the ligation of both LLT1 binding interfaces leads to effective NKR-P1 inhibitory signaling. In summary, our findings collectively support a model of NKR-P1:LLT1 clustering, which allows the interacting proteins to overcome weak ligand-receptor affinity and to trigger signal transduction upon cellular contact in the immune synapse.

  • Organizational Affiliation

    Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 12800, Prague, Czech Republic.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Killer cell lectin-like receptor subfamily B member 1
A, B, C, D, E
A, B, C, D, E, F, G, H
146Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q12918 (Homo sapiens)
Explore Q12918 
Go to UniProtKB:  Q12918
PHAROS:  Q12918
GTEx:  ENSG00000111796 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12918
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth B]
L [auth B]
M [auth C]
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth C],
P [auth D],
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth G],
V [auth G],
W [auth H],
X [auth H]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.806α = 101.88
b = 68.404β = 100.72
c = 101.564γ = 100.64
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic15-15181S
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLG14009

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2023-03-08
    Changes: Database references, Structure summary
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description