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- PDB-3ff7: Structure of NK cell receptor KLRG1 bound to E-cadherin -

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Basic information

Entry
Database: PDB / ID: 3ff7
TitleStructure of NK cell receptor KLRG1 bound to E-cadherin
Components
  • Epithelial cadherin
  • Killer cell lectin-like receptor subfamily G member 1
KeywordsCell adhesion/Immune system / KLRG1-cadherin complex / Calcium / Cell adhesion / Cell junction / Cell membrane / Cleavage on pair of basic residues / Disease mutation / Glycoprotein / Membrane / Phosphoprotein / Polymorphism / Transmembrane / Alternative splicing / Lectin / Receptor / Signal-anchor / Cell adhesion-Immune system COMPLEX
Function / homology
Function and homology information


response to Gram-positive bacterium / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / Formation of definitive endoderm / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ...response to Gram-positive bacterium / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / Formation of definitive endoderm / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Adherens junctions interactions / catenin complex / Apoptotic cleavage of cell adhesion proteins / GTPase activating protein binding / cell-cell junction assembly / adherens junction organization / apical junction complex / ankyrin binding / negative regulation of cell-cell adhesion / cellular response to lithium ion / homophilic cell adhesion via plasma membrane adhesion molecules / lateral plasma membrane / RHO GTPases activate IQGAPs / Integrin cell surface interactions / cellular defense response / cell adhesion molecule binding / synapse assembly / InlA-mediated entry of Listeria monocytogenes into host cells / Degradation of the extracellular matrix / negative regulation of cell migration / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / trans-Golgi network / cell morphogenesis / cytoplasmic side of plasma membrane / response to toxic substance / beta-catenin binding / cell-cell adhesion / positive regulation of protein import into nucleus / neuron projection development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / actin cytoskeleton / lamellipodium / cell junction / signaling receptor activity / postsynapse / carbohydrate binding / regulation of gene expression / membrane => GO:0016020 / cell surface receptor signaling pathway / endosome / response to xenobiotic stimulus / cadherin binding / inflammatory response / intracellular membrane-bounded organelle / innate immune response / glutamatergic synapse / calcium ion binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Killer cell lectin-like receptor subfamily G member 1 / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Natural killer cell receptor-like, C-type lectin-like domain / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin ...Killer cell lectin-like receptor subfamily G member 1 / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Natural killer cell receptor-like, C-type lectin-like domain / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / 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 / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Cadherin-1 / Killer cell lectin-like receptor subfamily G member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epithelial cadherin
B: Epithelial cadherin
C: Killer cell lectin-like receptor subfamily G member 1
D: Killer cell lectin-like receptor subfamily G member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2545
Polymers48,1944
Non-polymers601
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.120, 83.411, 56.508
Angle α, β, γ (deg.)90.000, 106.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Epithelial cadherin / E-cadherin / Cadherin-1 / Uvomorulin / CAM 120/80 / E-Cad/CTF1 / E-Cad/CTF2 / E-Cad/CTF3


Mass: 11124.637 Da / Num. of mol.: 2 / Fragment: UNP residues 155-253, Cadherin 1 domain / Mutation: C9L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH1, CDHE, UVO / Production host: Escherichia coli (E. coli) / References: UniProt: P12830
#2: Protein Killer cell lectin-like receptor subfamily G member 1 / Mast cell function-associated antigen / MAFA-like receptor / ITIM-containing receptor MAFA-L / C- ...Mast cell function-associated antigen / MAFA-like receptor / ITIM-containing receptor MAFA-L / C-type lectin domain family 15 member A


Mass: 12972.562 Da / Num. of mol.: 2 / Fragment: UNP residues 75-186, C-type lectin domain / Mutation: C131S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLRG1, CLEC15A, MAFA, MAFAL / Production host: Escherichia coli (E. coli) / References: UniProt: Q96E93
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6 / Details: PEG4000, pH 4.6, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.502 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 57098 / % possible obs: 98.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.064 / Χ2: 1.289 / Net I/σ(I): 21.542
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.714.90.56351041.00288.3
1.71-1.786.50.44356791.02798.6
1.78-1.867.30.31557381.042100
1.86-1.967.40.20658071.142100
1.96-2.087.50.12157781.206100
2.08-2.247.50.08957771.222100
2.24-2.467.40.0757961.189100
2.46-2.827.50.05657831.115100
2.82-3.557.40.05258201.14499.9
3.55-309.60.05858162.28398.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.71 Å
Translation2.5 Å27.71 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FF7

3ff7


Resolution: 1.8→30 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.246 1340 3 %
Rwork0.214 --
obs-44610 99.8 %
Solvent computationBsol: 35.739 Å2
Displacement parametersBiso max: 64.81 Å2 / Biso mean: 28.672 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.125 Å20 Å2-0.121 Å2
2--3.401 Å20 Å2
3----3.276 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 0 313 3648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.559
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3acy.param

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