3M9Z | pdb_00003m9z

Crystal Structure of extracellular domain of mouse NKR-P1A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.239 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Molecular architecture of mouse activating NKR-P1 receptors.

Kolenko, P.Rozbesky, D.Vanek, O.Kopecky, V.Hofbauerova, K.Novak, P.Pompach, P.Hasek, J.Skalova, T.Bezouska, K.Dohnalek, J.

(2011) J Struct Biol 175: 434-441

  • DOI: https://doi.org/10.1016/j.jsb.2011.05.001
  • Primary Citation Related Structures: 
    3M9Z

  • PubMed Abstract: 

    Receptors belonging to NKR-P1 family and their specific Clr ligands form an alternative missing self recognition system critical in immunity against tumors and viruses, elimination of tumor cells subjected to genotoxic stress, activation of T cell dependent immune response, and hypertension. The three-dimensional structure of the extracellular domain of the mouse natural killer (NK) cell receptor mNKR-P1Aex has been determined by X-ray diffraction. The core of the C-type lectin domain (CTLD) is homologous to the other CTLD receptors whereas one quarter of the domain forms an extended loop interacting tightly with a neighboring loop in the crystal. This domain swapping mechanism results in a compact interaction interface. A second dimerization interface resembles the known arrangement of other CTLD NK receptors. A functional dimeric form of the receptor is suggested, with the loop, evolutionarily conserved within this family, proposed to participate in interactions with ligands.


  • Organizational Affiliation
    • Institute of Macromolecular Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Heyrovského náměstí 2, 16206 Prague 6, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 16.1 kDa 
  • Atom Count: 1,134 
  • Modeled Residue Count: 124 
  • Deposited Residue Count: 139 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Killer cell lectin-like receptor subfamily B member 1A139Mus musculusMutation(s): 2 
Gene Names: Klrb1aLy55Ly55aNkrp1a
UniProt
Find proteins for P27811 (Mus musculus)
Explore P27811 
Go to UniProtKB:  P27811
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27811
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.239 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.912α = 90
b = 59.912β = 90
c = 159.303γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
BALBESphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-02-18
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-27
    Changes: Structure summary