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- PDB-3ff9: Structure of NK cell receptor KLRG1 -

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Basic information

Entry
Database: PDB / ID: 3ff9
TitleStructure of NK cell receptor KLRG1
ComponentsKiller cell lectin-like receptor subfamily G member 1
KeywordsIMMUNE SYSTEM / Natural Killer cell receptor KLTG1 / Glycoprotein / Lectin / Membrane / Phosphoprotein / Receptor / Signal-anchor / Transmembrane
Function / homology
Function and homology information


carbohydrate binding / cell surface receptor signaling pathway / intracellular membrane-bounded organelle / innate immune response / plasma membrane
Similarity search - Function
Killer cell lectin-like receptor subfamily G member 1 / Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...Killer cell lectin-like receptor subfamily G member 1 / Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Killer cell lectin-like receptor subfamily G member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLi, Y. / Mariuzza, R.A.
CitationJournal: Immunity / Year: 2009
Title: Structure of natural killer cell receptor KLRG1 bound to E-cadherin reveals basis for MHC-independent missing self recognition.
Authors: Li, Y. / Hofmann, M. / Wang, Q. / Teng, L. / Chlewicki, L.K. / Pircher, H. / Mariuzza, R.A.
History
DepositionDec 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Killer cell lectin-like receptor subfamily G member 1
B: Killer cell lectin-like receptor subfamily G member 1


Theoretical massNumber of molelcules
Total (without water)26,5652
Polymers26,5652
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Killer cell lectin-like receptor subfamily G member 1


Theoretical massNumber of molelcules
Total (without water)13,2821
Polymers13,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Killer cell lectin-like receptor subfamily G member 1


Theoretical massNumber of molelcules
Total (without water)13,2821
Polymers13,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.130, 56.930, 68.090
Angle α, β, γ (deg.)90.000, 97.200, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-8-

HOH

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Components

#1: Protein Killer cell lectin-like receptor subfamily G member 1 / Mast cell function-associated antigen 2F1 / Mast cell function-associated antigen


Mass: 13282.296 Da / Num. of mol.: 2 / Fragment: UNP residues 75-188, C-type lectin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klrg1, Mafa / Production host: Escherichia coli (E. coli) / References: UniProt: O88713
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8 / Details: Na,KPO4, pH 8.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 24208 / % possible obs: 97.7 % / Redundancy: 3.23 % / Rmerge(I) obs: 0.057 / Χ2: 0.99 / Scaling rejects: 592
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.7-1.762.980.3432.8693423201.1494.7
1.76-1.833.250.2863.4764423481.0995.6
1.83-1.913.240.2314774723881.0696.6
1.91-2.023.250.1745785024071.0697.3
2.02-2.143.270.1286.778802405197.9
2.14-2.313.230.1157.8794824340.9698.3
2.31-2.543.250.0811.2800024440.9798.9
2.54-2.913.310.0613820124690.8999.2
2.91-3.663.30.04417.8820224700.8599.6
3.66-29.333.220.03226.1842625230.999

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_BRF

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1B6E AND 1E87

1b6e

1e87


Resolution: 1.8→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.257 1009 4.8 %
Rwork0.223 --
obs-20475 98 %
Solvent computationBsol: 53.07 Å2
Displacement parametersBiso max: 74.83 Å2 / Biso mean: 23.182 Å2 / Biso min: 11.75 Å2
Baniso -1Baniso -2Baniso -3
1--4.899 Å20 Å2-2.451 Å2
2--2.998 Å20 Å2
3---1.901 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 0 169 2030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.253
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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