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- PDB-4pp8: Crystal structure of murine NK cell ligand RAE-1 beta in complex ... -

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Basic information

Entry
Database: PDB / ID: 4pp8
TitleCrystal structure of murine NK cell ligand RAE-1 beta in complex with NKG2D
Components
  • NKG2-D type II integral membrane protein
  • Retinoic acid early-inducible protein 1-beta
KeywordsIMMUNE SYSTEM / MURINE NK CELL LIGAND / RAE-1 BETA / NKG2D / MHC-I PLATFORM
Function / homology
Function and homology information


positive regulation of immune response to tumor cell / susceptibility to natural killer cell mediated cytotoxicity / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / positive regulation of natural killer cell activation / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of macrophage activation / natural killer cell activation / DAP12 signaling ...positive regulation of immune response to tumor cell / susceptibility to natural killer cell mediated cytotoxicity / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / positive regulation of natural killer cell activation / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of macrophage activation / natural killer cell activation / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / natural killer cell mediated cytotoxicity / cellular response to exogenous dsRNA / 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 / cellular response to lipopolysaccharide / carbohydrate binding / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / defense response to bacterium / external side of plasma membrane / cell surface / identical protein binding / plasma membrane
Similarity search - Function
Retinoic acid early-inducible protein 1 / Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2 / 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) ...Retinoic acid early-inducible protein 1 / Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2 / 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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / : / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Retinoic acid early-inducible protein 1-beta / 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
AuthorsLi, P. / Strong, R.K.
Citation
Journal: Immunity / Year: 2002
Title: Crystal structures of RAE-1beta and its complex with the activating immunoreceptor NKG2D.
Authors: Li, P. / McDermott, G. / Strong, R.K.
#1: Journal: Immunity / Year: 2000
Title: Retinoic acid early inducible genes define a ligand family for the activating NKG2D receptor in mice.
Authors: Cerwenka, A. / Bakker, A.B. / McClanahan, T. / Wagner, J. / Wu, J. / Phillips, J.H. / Lanier, L.L.
#2: Journal: Nat.Immunol. / Year: 2000
Title: Ligands for the murine NKG2D receptor: expression by tumor cells and activation of NK cells and macrophages.
Authors: Diefenbach, A. / Jamieson, A.M. / Liu, S.D. / Shastri, N. / Raulet, D.H.
History
DepositionFeb 26, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionApr 9, 2014ID: 1JSK
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NKG2-D type II integral membrane protein
B: NKG2-D type II integral membrane protein
C: Retinoic acid early-inducible protein 1-beta
D: Retinoic acid early-inducible protein 1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9305
Polymers68,8384
Non-polymers921
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.637, 58.637, 350.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALAA108 - 2321 - 125
21METMETVALVALBB108 - 2321 - 125
12HISHISGLNGLNCC3 - 1703 - 170
22HISHISGLNGLNDD3 - 1703 - 170

NCS ensembles :
ID
1
2

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Components

#1: Protein NKG2-D type II integral membrane protein / Killer cell lectin-like receptor subfamily K member 1 / NK cell receptor D / NKG2-D-activating NK receptor


Mass: 14375.146 Da / Num. of mol.: 2 / Fragment: RAE-1BETA, UNP residues 109-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Klrk1, Nkg2d, RAE-1 BETA / Plasmid: PET22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: O54709
#2: Protein Retinoic acid early-inducible protein 1-beta / RAE-1-beta


Mass: 20043.744 Da / Num. of mol.: 2 / Fragment: IMMUNORECEPTOR NKG2D, UNP residues 31-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: NKG2D, Raet1b / Plasmid: PET22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: O08603
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG8000, 0.300M AS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2003
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→48.77 Å / Num. all: 49287 / Num. obs: 45094 / % possible obs: 91.48 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.77 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.248 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.167 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 2285 5.1 %RANDOM
Rwork0.19049 ---
obs0.1918 42805 91.46 %-
all-49287 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.029 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å20 Å2
3----2.57 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4335 0 6 187 4528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024467
X-RAY DIFFRACTIONr_bond_other_d0.0030.023982
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9326072
X-RAY DIFFRACTIONr_angle_other_deg0.9339173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12625.403211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09515728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2611510
X-RAY DIFFRACTIONr_chiral_restr0.070.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215092
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021066
X-RAY DIFFRACTIONr_mcbond_it1.2912.8732177
X-RAY DIFFRACTIONr_mcbond_other1.2912.8732176
X-RAY DIFFRACTIONr_mcangle_it2.1814.292706
X-RAY DIFFRACTIONr_mcangle_other2.184.2912707
X-RAY DIFFRACTIONr_scbond_it1.3612.9722290
X-RAY DIFFRACTIONr_scbond_other1.3592.9722290
X-RAY DIFFRACTIONr_scangle_other2.2044.4123366
X-RAY DIFFRACTIONr_long_range_B_refined5.10423.1565142
X-RAY DIFFRACTIONr_long_range_B_other5.05122.9755094
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A67530.11
12B67530.11
21C74270.13
22D74270.13
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 80 -
Rwork0.237 1634 -
obs--47.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9338-0.5804-0.87831.88420.09735.19480.0826-0.04070.00320.00160.0776-0.09460.04240.1099-0.16020.03590.01820.00630.0151-0.00120.01460.37150.135214.0285
20.645-0.06110.44291.2391-1.05044.79950.06250.039-0.0821-0.11340.0502-0.06510.29330.1401-0.11270.10570.04790.02790.0431-0.00190.03652.81370.5466-11.2202
34.0992-0.4901-0.8134.0881-0.1565.053-0.15590.0581-0.05020.09490.09350.35690.1308-0.44060.06240.04460.02420.06340.07220.05270.1134-13.420420.497-1.2496
40.7113-1.1479-0.67646.2609-2.29943.40770.05940.1517-0.1774-0.56460.090.5640.2669-0.5496-0.14940.1942-0.0877-0.08140.2680.10420.291624.419922.54835.7475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A108 - 232
2X-RAY DIFFRACTION2B108 - 232
3X-RAY DIFFRACTION3C3 - 170
4X-RAY DIFFRACTION4D3 - 172

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