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- PDB-1mpu: Crystal Structure of the free human NKG2D immunoreceptor -

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Basic information

Entry
Database: PDB / ID: 1mpu
TitleCrystal Structure of the free human NKG2D immunoreceptor
ComponentsNKG2-D type II integral membrane protein
KeywordsIMMUNE SYSTEM / C-type lectin-like domain
Function / homology
Function and homology information


negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / T cell costimulation / nitric oxide biosynthetic process ...negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / T cell costimulation / nitric oxide biosynthetic process / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / DAP12 signaling / signaling receptor activity / carbohydrate binding / cellular response to lipopolysaccharide / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / external side of plasma membrane / cell surface / signal transduction / identical protein binding / membrane / 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
PHOSPHATE ION / NKG2-D type II integral membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMcFarland, B.J. / Kortemme, T. / Baker, D. / Strong, R.K.
CitationJournal: Structure / Year: 2003
Title: Symmetry Recognizing Asymmetry: Analysis of the Interactions between the C-Type Lectin-like Immunoreceptor NKG2D and MHC Class I-like Ligands
Authors: McFarland, B.J. / Kortemme, T. / Yu, S.F. / Baker, D. / Strong, R.K.
History
DepositionSep 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NKG2-D type II integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0762
Polymers15,9811
Non-polymers951
Water1,892105
1
A: NKG2-D type II integral membrane protein
hetero molecules

A: NKG2-D type II integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1524
Polymers31,9622
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3210 Å2
ΔGint-35 kcal/mol
Surface area13030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.650, 87.650, 36.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a homodimer is generated by the two-fold axis: 1/2+x, 1/2-y, 3/4-z.

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Components

#1: Protein NKG2-D type II integral membrane protein / NKG2-D activating NK receptor / NK cell receptor D


Mass: 15981.102 Da / Num. of mol.: 1 / Fragment: residues 80-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P26718
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium dihydrogen phosphate, bicine, ethylene glycol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlhuNKG2D1drop
24 mg/mlULBP11drop
325 mMPIPES1droppH7.0
4150 mM1dropNaCl
51 mMEDTA1drop
60.02 %1dropNaN3
71.6 Mammonium dihydrogen phosphate/diammonium hydrogen phosphate1reservoir
810 %ethylene glycol1reservoir
9100 mMBicine1reservoirpH9.0

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 5, 2001 / Details: Osmics mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 5240 / Num. obs: 5057 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.1 % / Rsym value: 0.066 / Net I/σ(I): 20.2
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 6.8 / Num. unique all: 517 / Rsym value: 0.199 / % possible all: 90.1
Reflection
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 90.1 % / Num. unique obs: 466 / Rmerge(I) obs: 0.199

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HYR (CHAIN A)

1hyr


Resolution: 2.5→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 498 -random
Rwork0.245 ---
all-5057 --
obs-4838 95.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-20.861 Å2--
2--14.583 Å2-
3----35.444 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 5 105 1139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d1.4
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection
Rfree0.5083 38
Rwork0.3623 -
obs-421
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 2.5 Å

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