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- PDB-1hq8: CRYSTAL STRUCTURE OF THE MURINE NK CELL-ACTIVATING RECEPTOR NKG2D... -

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Basic information

Entry
Database: PDB / ID: 1hq8
TitleCRYSTAL STRUCTURE OF THE MURINE NK CELL-ACTIVATING RECEPTOR NKG2D AT 1.95 A
ComponentsNKG2-D
KeywordsAPOPTOSIS / homodimer / cis-proline
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell activation / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway ...positive regulation of myeloid dendritic cell activation / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / nitric oxide biosynthetic process / kinase binding / positive regulation of type II interferon production / positive regulation of nitric oxide biosynthetic process / signaling receptor activity / carbohydrate binding / cellular response to lipopolysaccharide / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / positive regulation of apoptotic process / external side of plasma membrane / cell surface / identical protein binding / plasma membrane
Similarity search - Function
NKG2-D type II integral membrane protein / 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 ...NKG2-D type II integral membrane protein / 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
NKG2-D type II integral membrane protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWolan, D.W. / Teyton, L. / Rudolph, M.G. / Villmow, B. / Bauer, S. / Busch, D.H. / Wilson, I.A.
CitationJournal: Nat.Immunol. / Year: 2001
Title: Crystal structure of the murine NK cell-activating receptor NKG2D at 1.95 A.
Authors: Wolan, D.W. / Teyton, L. / Rudolph, M.G. / Villmow, B. / Bauer, S. / Busch, D.H. / Wilson, I.A.
History
DepositionDec 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NKG2-D


Theoretical massNumber of molelcules
Total (without water)14,1151
Polymers14,1151
Non-polymers00
Water1,38777
1
A: NKG2-D

A: NKG2-D


Theoretical massNumber of molelcules
Total (without water)28,2302
Polymers28,2302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Unit cell
Length a, b, c (Å)49.860, 85.190, 87.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x, 1/2-y, z

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Components

#1: Protein NKG2-D


Mass: 14114.836 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: O54709
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NaCl, Na-Cit., PEG400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17 mg/mlprotein1drop
22.3 M1reservoirNaCl
30.15 Msodium citrate1reservoirpH6.5
45 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 13874 / % possible obs: 98.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1361 / % possible all: 97.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 13874
Reflection shell
*PLUS
% possible obs: 97.7 % / Num. unique obs: 1361

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→27.62 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 6848118.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1340 10.2 %RANDOM
Rwork0.215 ---
obs0.215 13099 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.44 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---6.16 Å20 Å2
3---6.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.95→27.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms986 0 0 77 1063
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.652.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.326 188 9.6 %
Rwork0.293 1762 -
obs--85 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.326 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.293 / Rfactor obs: 0.293

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