7ODU

Natural killer cell receptor NKR-P1B from Rattus norvegicus in complex with its cognate ligand Clr-11

• PDB DOI: https://doi.org/10.2210/pdb7ODU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Rattus norvegicus
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2021-04-30 Released: 2022-06-01 
• Deposition Author(s): Skalova, T., Blaha, J., Kalouskova, B., Skorepa, O., Vanek, O., Dohnalek, J.
• Funding Organization(s): Czech Science Foundation, Ministry of Education, Youth and Sports of the Czech Republic

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Literature

Natural killer cell receptor NKR-P1B from Rattus norvegicus in complex with its cognate ligand Clr-11

Skalova, T., Vanek, O., Kalouskova, B., Skorepa, O., Blaha, J., Harlos, K., Dohnalek, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 49.88 kDa 
• Atom Count: 3,154 
• Modelled Residue Count: 372 
• Deposited Residue Count: 417 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin domain family 2 member D11	A, B	133	Rattus norvegicus	Mutation(s): 1  Gene Names: Clec2d11, Clrb, Ocil
UniProt
Find proteins for Q0H8B9 (Rattus norvegicus) Explore Q0H8B9  Go to UniProtKB:  Q0H8B9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Killer cell lectin-like receptor subfamily B member 1B allele A	C	151	Rattus norvegicus	Mutation(s): 0  Gene Names: Klrb1b, Nkrp1b
UniProt
Find proteins for A4KWA1 (Rattus norvegicus) Explore A4KWA1  Go to UniProtKB:  A4KWA1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], H [auth B], I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.593	α = 90
b = 111.593	β = 90
c = 110.107	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
BALBES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Skalova, T., Blaha, J., Kalouskova, B., Skorepa, O., Vanek, O., Dohnalek, J.

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Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	18-10687S
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	CZ.02.1.01/0.0/0.0/16_013/0001776

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description