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- PDB-1fo0: MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULE COMPLEX -

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Entry
Database: PDB / ID: 1fo0
TitleMURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULE COMPLEX
Components
  • (PROTEIN (BM3.3 T CELL RECEPTOR ...) x 2
  • NATURALLY PROCESSED OCTAPEPTIDE PBM1
  • PROTEIN (ALLOGENEIC H-2KB MHC CLASS I MOLECULE)
  • PROTEIN (BETA-2 MICROGLOBULIN)
KeywordsIMMUNE SYSTEM / T CELL RECEPTOR / CLASS I MHC / H-2KB / TCR-PMHC COMPLEX
Function / homology
Function and homology information


TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / inner ear development / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / positive regulation of phosphorylation / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis
Similarity search - Function
BTBD10/KCTD20, BTB/POZ domain / BTBD10/KCTD20 / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / 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 ...BTBD10/KCTD20, BTB/POZ domain / BTBD10/KCTD20 / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / 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 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / 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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
: / : / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / T-cell receptor beta chain V region E1 / TRADV16D / BTB/POZ domain-containing protein KCTD20
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsReiser, J.B. / Darnault, C. / Guimezanes, A. / Gregoire, C. / Mosser, T. / Schmitt-Verhulst, A.-M. / Fontecilla-Camps, J.C. / Malissen, B. / Housset, D. / Mazza, G.
Citation
Journal: Nat.Immunol. / Year: 2000
Title: Crystal structure of a T cell receptor bound to an allogeneic 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.
#1: Journal: Embo J. / Year: 1997
Title: The Three-Dimensional Structure of a T Cell Receptor Valpha-Vbeta 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: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Crystal Structure of an H-2Kb-Ovalbumin Peptide Com Reveals the Interplay of Primary and Secondary Anchor Positions in the Major Histocompatibility Complex Binding Groove
Authors: Fremont, D.H. / Stura, E.A. / Matsumura, M. / Peterson, P.A. / Wilson, I.A.
#3: Journal: Science / Year: 1998
Title: Structural Basis of Plasticity in T Cell Receptor Recognition of a Self Peptide-Mhc Antigen
Authors: Garcia, K.C. / Degano, M. / Pease, L.R. / Huang, M. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
#4: Journal: Nature / Year: 1996
Title: Structure of the Complex between Human T Cell Receptor, Viral Peptide and Hla-A2
Authors: Garboczi, D.N. / Ghosh, P. / Utz, U. / Fan, Q.R. / Bidisson, W.E. / Wiley, D.
#5: Journal: Immunity / Year: 1998
Title: Two Human T Cell Receptors Bind in a Similar Mode To the Hla-A2/Tax Peptide Complex Using Different Tcr Amino-acids
Authors: Ding, Y.H. / Smith, K.J. / Garboczi, D.N. / Utz, U. / Bidisson, W.E. / Wiley, D.C.
#6: Journal: Int.Immunol. / Year: 1991
Title: Each of Two Productive T Cell Receptor Alpha-Gene Rearrangements Found in Both the A10 and Bm3.3 Cell Clones Give Rise to an Alpha Chain which Can Contribute to the Constitution of a Surface- ...Title: Each of Two Productive T Cell Receptor Alpha-Gene Rearrangements Found in Both the A10 and Bm3.3 Cell Clones Give Rise to an Alpha Chain which Can Contribute to the Constitution of a Surface-Expressed Alpha-Beta Dimer
Authors: Couez, D. / Malissen, M. / Buferne, M. / Schmitt-Verhulst, A.-M. / Malissen, B.
History
DepositionAug 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Database references / Structure summary
Revision 1.4Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PROTEIN (ALLOGENEIC H-2KB MHC CLASS I MOLECULE)
L: PROTEIN (BETA-2 MICROGLOBULIN)
P: NATURALLY PROCESSED OCTAPEPTIDE PBM1
A: PROTEIN (BM3.3 T CELL RECEPTOR ALPHA-CHAIN)
B: PROTEIN (BM3.3 T CELL RECEPTOR BETA-CHAIN)


Theoretical massNumber of molelcules
Total (without water)70,5085
Polymers70,5085
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.580, 120.420, 102.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules HL

#1: Protein PROTEIN (ALLOGENEIC H-2KB MHC CLASS I MOLECULE)


Mass: 31908.629 Da / Num. of mol.: 1 / 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: UniProt: P01901
#2: Protein PROTEIN (BETA-2 MICROGLOBULIN)


Mass: 11704.359 Da / Num. of mol.: 1
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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PROTEIN (BM3.3 T CELL RECEPTOR ... , 2 types, 2 molecules AB

#4: Protein PROTEIN (BM3.3 T CELL RECEPTOR ALPHA-CHAIN)


Mass: 12945.639 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT, VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): MYELOMA CELLS / Production host: Mus musculus (house mouse) / References: GenBank: 201157, UniProt: Q5R1F1*PLUS
#5: Protein PROTEIN (BM3.3 T CELL RECEPTOR BETA-CHAIN)


Mass: 12965.832 Da / Num. of mol.: 1 / Fragment: FV FRAGMENT, VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): MYELOMA CELLS / Production host: Mus musculus (house mouse) / References: GenBank: 554307, UniProt: P04214*PLUS

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Protein/peptide / Non-polymers , 2 types, 192 molecules P

#3: Protein/peptide NATURALLY PROCESSED OCTAPEPTIDE PBM1


Mass: 983.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE NATURALLY OCCURS IN MUS MUCULUS / References: UniProt: Q8CDD8*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 62 % / Description: RESOLUTION RANGE USED FOR MR 15.0-3.5 A
Crystal growMethod: vapor diffusion / pH: 7
Details: PEG 6000 10% HEPES 0.1M PH 7.0 MGAC 0.25 M NACL 0.25M, pH 7.00, VAPOR DIFFUSION
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
210 %PEG60001reservoir
30.1 MHEPES1reservoir
40.25 Mmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.5→23.1 Å / Num. obs: 33614 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 49.87 Å2 / Rsym value: 0.081 / Net I/σ(I): 8.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.375 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.375

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC4refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1KB5, 1VAC

1kb5

1vac


Resolution: 2.5→12 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION USED R V
RfactorNum. reflection% reflectionSelection details
Rfree0.276 3300 10 %RANDOM
Rwork0.225 ---
obs0.218 32832 100 %-
Displacement parametersBiso mean: 57.93 Å2
Refinement stepCycle: LAST / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4948 0 0 191 5139
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.030.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8662
X-RAY DIFFRACTIONp_mcangle_it3.463
X-RAY DIFFRACTIONp_scbond_it2.8573
X-RAY DIFFRACTIONp_scangle_it4.5164
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1720.2
X-RAY DIFFRACTIONp_singtor_nbd0.2040.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.27
X-RAY DIFFRACTIONp_staggered_tor19.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.220
X-RAY DIFFRACTIONp_special_tor

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