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- PDB-1kj2: Murine Alloreactive ScFv TCR-Peptide-MHC Class I Molecule Complex -

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Entry
Database: PDB / ID: 1kj2
TitleMurine Alloreactive ScFv TCR-Peptide-MHC Class I Molecule Complex
Components
  • (KB5-C20 T-Cell receptor ...) x 2
  • Allogeneic H-2Kb MHC Class I Molecule
  • Beta-2 microglobulin
  • Naturally processed octapeptide PKB1
KeywordsIMMUNE SYSTEM / T CELL RECEPTOR / CLASS I MHC / H-2KB / TCR-PMHC COMPLEX / ALLOGENEIC
Function / homology
Function and homology information


alpha-aminoacyl-tRNA binding / RNA surveillance / cytoplasmic exosome (RNase complex) / positive regulation of mRNA catabolic process / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions ...alpha-aminoacyl-tRNA binding / RNA surveillance / cytoplasmic exosome (RNase complex) / positive regulation of mRNA catabolic process / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / DAP12 signaling / cellular response to iron(III) ion / GTP metabolic process / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class Ib protein complex / protein-synthesizing GTPase / response to molecule of bacterial origin / regulation of erythrocyte differentiation / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / inner ear development / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / multicellular organismal-level iron ion homeostasis / regulation of membrane depolarization / CD8 receptor binding / TAP binding / endoplasmic reticulum exit site / T cell differentiation in thymus / translational elongation / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / translation elongation factor activity / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / Neutrophil degranulation / 14-3-3 protein binding / positive regulation of T cell mediated cytotoxicity / negative regulation of neuron projection development / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / protein refolding / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / late endosome membrane / cellular response to lipopolysaccharide / protein-folding chaperone binding / antimicrobial humoral immune response mediated by antimicrobial peptide / early endosome membrane / antibacterial humoral response / defense response to Gram-negative bacterium / amyloid fibril formation / protein homotetramerization / adaptive immune response / early endosome / intracellular iron ion homeostasis / learning or memory / cytoplasmic translation / tRNA binding / defense response to bacterium / defense response to Gram-positive bacterium / immune response / receptor ligand activity / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / lysosomal membrane / GTPase activity
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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / 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 / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 / T-cell receptor beta chain V region E1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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: Embo J. / Year: 1997
Title: The three-dimentional structure of a T-cell antigen receptor ValphaVbeta heterodimer reveals a novel arrangement of the Vbeta domain
Authors: Housset, D. / Mazza, G. / Gregoire, C. / Piras, C. / Malissen, B. / Fontecilla-Camps, J.C.
#2: Journal: NAT.IMMUNOL. / Year: 2000
Title: CRYSTAL STRUCTURE OF A T CELL RECEPTOR BOUND TO AN ALLOGENIC MHC MOLECULE
Authors: Reiser, J.-B. / Darnault, C. / Guimezanes, A. / Gregoire, C. / Mosser, T. / Schmitt-Verhulst, A.-M. / Fontecilla-Camps, J.C. / Malissen, B. / Housset, D. / Mazza, G.
#3: 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 CD8-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: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Allogeneic H-2Kb MHC Class I Molecule
P: Naturally processed octapeptide PKB1
L: Beta-2 microglobulin
A: KB5-C20 T-Cell receptor alpha-chain
B: KB5-C20 T-Cell receptor beta-chain
I: Allogeneic H-2Kb MHC Class I Molecule
Q: Naturally processed octapeptide PKB1
M: Beta-2 microglobulin
D: KB5-C20 T-Cell receptor alpha-chain
E: KB5-C20 T-Cell receptor beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,98013
Polymers140,97110
Non-polymers2,0103
Water1,63991
1
H: Allogeneic H-2Kb MHC Class I Molecule
P: Naturally processed octapeptide PKB1
L: Beta-2 microglobulin
A: KB5-C20 T-Cell receptor alpha-chain
B: KB5-C20 T-Cell receptor beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2747
Polymers70,4855
Non-polymers1,7892
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Allogeneic H-2Kb MHC Class I Molecule
Q: Naturally processed octapeptide PKB1
M: Beta-2 microglobulin
D: KB5-C20 T-Cell receptor alpha-chain
E: KB5-C20 T-Cell receptor beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7066
Polymers70,4855
Non-polymers2211
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.20, 77.92, 132.96
Angle α, β, γ (deg.)90.00, 108.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules HILM

#1: Protein Allogeneic H-2Kb MHC Class I Molecule / MHC class I heavy chain


Mass: 31971.664 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) / Production host: Escherichia coli (E. coli) / References: GenBank: 1644442, UniProt: P01901*PLUS
#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) / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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KB5-C20 T-Cell receptor ... , 2 types, 4 molecules ADBE

#4: Protein KB5-C20 T-Cell receptor alpha-chain / T-cell receptor alpha Variable Domain Alpha Chain


Mass: 12478.844 Da / Num. of mol.: 2 / Fragment: Fv fragment , variable domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / Keywords: www / References: GenBank: 554285
#5: Protein KB5-C20 T-Cell receptor beta-chain / T-cell receptor beta Variable Domain Alpha Chain


Mass: 13381.247 Da / Num. of mol.: 2 / Fragment: Fv fragment , variable domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / References: GenBank: 3114395, UniProt: P04214*PLUS

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Protein/peptide / Non-polymers , 2 types, 93 molecules PQ

#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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 3 molecules

#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1567.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-2-2-1-3-4/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1_g3-h2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 17-19% PEG 6000, 0.1M Mes, 0.1M NaCl, 0.1M MgAc, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
14.0 mg/mlprotein1drop
217-19 %PEG60001reservoir
30.1 MMES1reservoirpH6.7
40.1 M1reservoirNaCl
50.1 M1reservoirMgAc

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.987 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 19, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.71→14.99 Å / Num. all: 45992 / Num. obs: 45992 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 55.9 Å2 / Rsym value: 0.084 / Net I/σ(I): 7.7
Reflection shellResolution: 2.71→2.85 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2 / Num. unique all: 4916 / Rsym value: 0.382 / % possible all: 87.8
Reflection
*PLUS
Highest resolution: 2.7 Å / Rmerge(I) obs: 0.084

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KB5, 1KJ3

1kb5

1kj3


Resolution: 2.71→12 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The work R and Free R values correspond to the ones calulated in the last cycle of maximum likelihood refinement. Due to the resolution limit of our structure (2.7), The refinement has been ...Details: The work R and Free R values correspond to the ones calulated in the last cycle of maximum likelihood refinement. Due to the resolution limit of our structure (2.7), The refinement has been ended by few cycles of least-square method including all reflexions. So both distinct algorithms and the including of Free set in refinement can make the convergence a little different.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 4515 10 %RANDOM
Rwork0.22 ---
all0.219 44772 --
obs0.219 44772 --
Solvent computationBsol: 26.56 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 45.65 Å2
Baniso -1Baniso -2Baniso -3
1-5.4 Å20 Å29.8 Å2
2---9.7 Å20 Å2
3---4.3 Å2
Refinement stepCycle: LAST / Resolution: 2.71→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9919 0 134 91 10144
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.56
X-RAY DIFFRACTIONc_dihedral_angle_d26.34
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.972
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.71→2.81 Å
RfactorNum. reflection% reflection
Rfree0.385 383 11 %
Rwork0.362 3345 -
obs-3728 -
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.34
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
LS refinement shell
*PLUS
Rfactor obs: 0.362

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