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- PDB-1jfm: CRYSTAL STRUCTURE OF MURINE NK CELL LIGAND RAE-1 BETA -

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Basic information

Entry
Database: PDB / ID: 1jfm
TitleCRYSTAL STRUCTURE OF MURINE NK CELL LIGAND RAE-1 BETA
Componentsretinoic acid early transcript 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 / natural killer cell lectin-like receptor binding / positive regulation of natural killer cell activation / positive regulation of macrophage activation / cellular response to exogenous dsRNA / positive regulation of type II interferon production / positive regulation of nitric oxide biosynthetic process / cellular response to lipopolysaccharide / defense response to bacterium ...positive regulation of immune response to tumor cell / susceptibility to natural killer cell mediated cytotoxicity / natural killer cell lectin-like receptor binding / positive regulation of natural killer cell activation / positive regulation of macrophage activation / cellular response to exogenous dsRNA / positive regulation of type II interferon production / positive regulation of nitric oxide biosynthetic process / cellular response to lipopolysaccharide / defense response to bacterium / external side of plasma membrane / plasma membrane
Similarity search - Function
Retinoic acid early-inducible protein 1 / Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Retinoic acid early-inducible protein 1-beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.85 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 2 Activating Nkg2D Receptor in Mouse
Authors: CERWENKA, A. / BAKKER, A.B. / MCCLANHAN, 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 Macrophages
Authors: DIEFENBACH, A. / JAMIESON, A.M. / LIU, S.D. / SHASTRI, N. / RAULET, D.H.
History
DepositionJun 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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

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Assembly

Deposited unit
A: retinoic acid early transcript beta
B: retinoic acid early transcript beta
C: retinoic acid early transcript beta
D: retinoic acid early transcript beta
E: retinoic acid early transcript beta


Theoretical massNumber of molelcules
Total (without water)100,2195
Polymers100,2195
Non-polymers00
Water75742
1
A: retinoic acid early transcript beta


Theoretical massNumber of molelcules
Total (without water)20,0441
Polymers20,0441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: retinoic acid early transcript beta


Theoretical massNumber of molelcules
Total (without water)20,0441
Polymers20,0441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: retinoic acid early transcript beta


Theoretical massNumber of molelcules
Total (without water)20,0441
Polymers20,0441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: retinoic acid early transcript beta


Theoretical massNumber of molelcules
Total (without water)20,0441
Polymers20,0441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: retinoic acid early transcript beta


Theoretical massNumber of molelcules
Total (without water)20,0441
Polymers20,0441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.415, 138.415, 337.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein
retinoic acid early transcript beta / Rae-1 beta


Mass: 20043.744 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: RAE-1beta / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: O08603
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.9 Å3/Da / Density % sol: 68.5 % / Description: MIR WITH 5 FOLD NCS AVERAGING
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% PEG400 + 375mM (NH4)2SO4, pH 4.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
225 mMPIPES1drop
31 mMEDTA1drop
40.02 %1droppH7.0NaN3
530 %(w/w)PEG4001reservoir
60.375 Mammonium sulfate1reservoir
7100 mMacetate1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2001 / Details: DOUBLE CRYSTAL
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.11
ReflectionResolution: 2.85→25 Å / Num. all: 38675 / Num. obs: 37491 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.37 % / Biso Wilson estimate: 88.9 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 37.5
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 11 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1899 / Rsym value: 0.46 / % possible all: 100
Reflection
*PLUS
Num. obs: 38675 / Redundancy: 10.4 % / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNS1refinement
CCP4phasing
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2.85→24.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 283690.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2839 7.6 %RANDOM
Rwork0.234 ---
all0.237 38675 --
obs0.234 37491 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.82 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 89 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.85→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7025 0 0 42 7067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.05
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 453 7.8 %
Rwork0.398 5328 -
obs-5781 91.1 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 7.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 89 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05
LS refinement shell
*PLUS
Rfactor Rfree: 0.403 / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.398

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