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- PDB-1je6: Structure of the MHC Class I Homolog MICB -

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Basic information

Entry
Database: PDB / ID: 1je6
TitleStructure of the MHC Class I Homolog MICB
ComponentsMHC class I chain-related protein
KeywordsIMMUNE SYSTEM / DELTA-TCR / GLYCOPROTEIN / SIGNA IMMUNOGLOBULIN FOLD / T-CELL
Function / homology
Function and homology information


immune response-activating cell surface receptor signaling pathway / natural killer cell lectin-like receptor binding / negative regulation of defense response to virus by host / cytolysis / gamma-delta T cell activation / regulation of immune response / response to retinoic acid / viral process / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib ...immune response-activating cell surface receptor signaling pathway / natural killer cell lectin-like receptor binding / negative regulation of defense response to virus by host / cytolysis / gamma-delta T cell activation / regulation of immune response / response to retinoic acid / viral process / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to heat / adaptive immune response / killing of cells of another organism / response to oxidative stress / membrane => GO:0016020 / immune response / external side of plasma membrane / signaling receptor binding / cell surface / extracellular space / plasma membrane
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I polypeptide-related sequence B / MHC class I polypeptide-related sequence B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHolmes, M.A. / Li, P. / Strong, R.K.
CitationJournal: J.Immunol. / Year: 2002
Title: Structural studies of allelic diversity of the MHC class I homolog MIC-B, a stress-inducible ligand for the activating immunoreceptor NKG2D.
Authors: Holmes, M.A. / Li, P. / Petersdorf, E.W. / Strong, R.K.
History
DepositionJun 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I chain-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8775
Polymers31,4931
Non-polymers3844
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MHC class I chain-related protein
hetero molecules

A: MHC class I chain-related protein
hetero molecules

A: MHC class I chain-related protein
hetero molecules

A: MHC class I chain-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,50920
Polymers125,9724
Non-polymers1,53716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area14860 Å2
ΔGint-245 kcal/mol
Surface area48540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.700, 81.700, 86.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein MHC class I chain-related protein / MICB


Mass: 31492.938 Da / Num. of mol.: 1 / Fragment: Extra-cellular domain (residues 1-274)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICB / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P79525, UniProt: Q29980*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 mg/mlprotein1drop
21.2 Mammonium sulfate1reservoir
350 mMTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.10, 0.97953, 0.9793, 0.9567
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2000
RadiationMonochromator: synchrotron wiggler station / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.979531
30.97931
40.95671
ReflectionResolution: 2.5→50 Å / Num. all: 10656 / Num. obs: 10656 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.62 / Net I/σ(I): 49.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 6.8 / Num. unique all: 1037 / % possible all: 100
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2976 1074 10 %random
Rwork0.2546 ---
all0.2588 10459 --
obs0.2588 10459 98.4 %-
Displacement parametersBiso mean: 43.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 20 0 2191
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.1
LS refinement shellResolution: 2.5→2.59 Å /
RfactorNum. reflection
Rfree0.4033 84
Rwork0.3555 872
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.255
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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