4QKI | pdb_00004qki

Dimeric form of human LLT1, a ligand for NKR-P1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.244 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history

Literature

Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states

Skalova, T.Blaha, J.Harlos, K.Duskova, J.Koval, T.Stransky, J.Hasek, J.Vanek, O.Dohnalek, J.

(2015) Acta Crystallogr D Biol Crystallogr 71: 578-591

  • DOI: https://doi.org/10.1107/S1399004714027928
  • Primary Citation Related Structures: 
    4QKG, 4QKH, 4QKI, 4QKJ

  • PubMed Abstract: 

    Human LLT1 is a C-type lectin-like ligand of NKR-P1 (CD161, gene KLRB1), a C-type lectin-like receptor of natural killer cells. Using X-ray diffraction, the first experimental structures of human LLT1 were determined. Four structures of LLT1 under various conditions were determined: monomeric, dimeric deglycosylated after the first N-acetylglucosamine unit in two forms and hexameric with homogeneous GlcNAc2Man5 glycosylation. The dimeric form follows the classical dimerization mode of human CD69. The monomeric form keeps the same fold with the exception of the position of an outer part of the long loop region. The hexamer of glycosylated LLT1 consists of three classical dimers. The hexameric packing may indicate a possible mode of interaction of C-type lectin-like proteins in the glycosylated form.


  • Organizational Affiliation
    • Institute of Biotechnology, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20 Praha 4, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 32.27 kDa 
  • Atom Count: 2,228 
  • Modeled Residue Count: 242 
  • Deposited Residue Count: 270 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-type lectin domain family 2 member D
A, B
135Homo sapiensMutation(s): 1 
Gene Names: CLAXCLEC2BCLEC2DLLT1OCIL
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHP7 (Homo sapiens)
Explore Q9UHP7 
Go to UniProtKB:  Q9UHP7
PHAROS:  Q9UHP7
GTEx:  ENSG00000069493 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHP7
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q9UHP7-1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.244 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.26α = 90
b = 54.12β = 90
c = 74.22γ = 90
Software Package:
Software NamePurpose
BALBESphasing
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 1.2: 2018-06-13
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-10-16
    Changes: Structure summary