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- PDB-1kj3: Mhc Class I H-2Kb molecule complexed with pKB1 peptide -

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Basic information

Entry
Database: PDB / ID: 1kj3
TitleMhc Class I H-2Kb molecule complexed with pKB1 peptide
Components
  • BETA-2 MICROGLOBULIN
  • H-2KB MHC CLASS I MOLECULE ALPHA CHAIN
  • NATURALLY PROCESSED OCTAPEPTIDE PKB1
KeywordsIMMUNE SYSTEM / MHC CLASS I / H-2KB / PMHC COMPLEX / ALLOGENEIC
Function / homology
Function and homology information


alpha-aminoacyl-tRNA binding / cytoplasmic exosome (RNase complex) / positive regulation of mRNA catabolic process / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / GTP metabolic process / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell ...alpha-aminoacyl-tRNA binding / cytoplasmic exosome (RNase complex) / positive regulation of mRNA catabolic process / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / GTP metabolic process / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / translation elongation factor activity / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / cytoplasmic translation / learning or memory / tRNA binding / defense response to bacterium / external side of plasma membrane / GTPase activity / GTP binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
GTP binding protein 1-like, GTP-binding domain / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. ...GTP binding protein 1-like, GTP-binding domain / : / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Translation protein, beta-barrel domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GTP-binding protein 1 / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsReiser, J.-B. / Gregoire, C. / Darnault, C. / Mosser, T. / Guimezanes, A. / Schmitt-Verhulst, A.-M. / Fontecilla-Camps, J.C. / Mazza, G. / Malissen, B. / Housset, D.
Citation
Journal: Immunity / Year: 2002
Title: A T cell receptor CDR3beta loop undergoes conformational changes of unprecedented magnitude upon binding to a peptide/MHC class I complex.
Authors: Reiser, J.B. / Gregoire, C. / Darnault, C. / Mosser, T. / Guimezanes, A. / Schmitt-Verhulst, A.M. / Fontecilla-Camps, J.C. / Mazza, G. / Malissen, B. / Housset, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Crystal structure of an H-2Kb-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove
Authors: Fremont, D. / Stura, E. / Matsumura, M. / Peterson, P. / Wilson, I.
#2: Journal: EUR.J.IMMUNOL. / Year: 2001
Title: IDENTIFICATION OF ENDOGENEOUS PEPTIDES RECOGNIZED BU IN VIVO OR IN VITRO GENERATED ALLOREACTIVE CTL: DISTINCT CHARACTERISTICS CORRELATED WITH CD-8 DEPENDENCE
Authors: Guimezanes, A. / Barret-Wilt, G. / Gulden-Thompson, P. / Shabanowitz, J. / Hunt, D. / Schmitt-Verhulst, A.-M.
History
DepositionDec 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: H-2KB MHC CLASS I MOLECULE ALPHA CHAIN
P: NATURALLY PROCESSED OCTAPEPTIDE PKB1
L: BETA-2 MICROGLOBULIN
I: H-2KB MHC CLASS I MOLECULE ALPHA CHAIN
Q: NATURALLY PROCESSED OCTAPEPTIDE PKB1
M: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)89,7076
Polymers89,7076
Non-polymers00
Water6,774376
1
H: H-2KB MHC CLASS I MOLECULE ALPHA CHAIN
P: NATURALLY PROCESSED OCTAPEPTIDE PKB1
L: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)44,8533
Polymers44,8533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-16 kcal/mol
Surface area19160 Å2
MethodPISA
2
I: H-2KB MHC CLASS I MOLECULE ALPHA CHAIN
Q: NATURALLY PROCESSED OCTAPEPTIDE PKB1
M: BETA-2 MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)44,8533
Polymers44,8533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-16 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.240, 90.630, 89.580
Angle α, β, γ (deg.)90.00, 111.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein H-2KB MHC CLASS I MOLECULE ALPHA CHAIN / H-2KB MHC CLASS I MOLECULE heavy chain


Mass: 32199.971 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS (ALPHA1, ALPHA2, ALPHA3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene (production host): H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#2: Protein/peptide NATURALLY PROCESSED OCTAPEPTIDE PKB1


Mass: 949.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SEQUENCE NATURALLY OCCURS IN MUS MUCULUS / References: UniProt: O08582
#3: Protein BETA-2 MICROGLOBULIN


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene (production host): B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5M K2HPO4/N2HPO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 Msodium potassium phosphate1droppH6.5
24.0 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.3→22.53 Å / Num. all: 43653 / Num. obs: 43653 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.046 / Net I/σ(I): 11.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 6306 / Rsym value: 0.161 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2.3 Å / Rmerge(I) obs: 0.046

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VAC

1vac


Resolution: 2.3→12 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 4278 10 %RANDOM
Rwork0.207 ---
all0.211 42902 --
obs0.211 42902 --
Displacement parametersBiso mean: 40.57 Å2
Baniso -1Baniso -2Baniso -3
1--4.9 Å20 Å20.3 Å2
2--12.1 Å20 Å2
3----6.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 0 376 6694
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0220.03
X-RAY DIFFRACTIONp_planar_d0.0270.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_plane_restr0.011
X-RAY DIFFRACTIONp_chiral_restr0.140.2
X-RAY DIFFRACTIONp_special_tor
X-RAY DIFFRACTIONp_planar_tor2.27
X-RAY DIFFRACTIONp_staggered_tor17.915
X-RAY DIFFRACTIONp_transverse_tor24.220
X-RAY DIFFRACTIONp_mcbond_it1.112
X-RAY DIFFRACTIONp_mcangle_it2.023
X-RAY DIFFRACTIONp_scbond_it2.033
X-RAY DIFFRACTIONp_scangle_it3.174
LS refinement shellResolution: 2.3→2.4 Å
RfactorNum. reflection
Rfree0.32 484
Rwork0.246 -
obs-4765
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.3
X-RAY DIFFRACTIONp_mcbond_it1.112
X-RAY DIFFRACTIONp_scbond_it2.033
X-RAY DIFFRACTIONp_mcangle_it2.023
X-RAY DIFFRACTIONp_scangle_it3.174

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