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

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Basic information

Entry
Database: PDB / ID: 1nam
TitleMURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULE COMPLEX
Components
  • (BM3.3 T Cell Receptor ...) x 2
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain precursor
  • Nucleocapsid
KeywordsIMMUNE SYSTEM / T cell receptor / class I MHC / H-2Kb / TCR-pMHC complex / alloreactivity / crossreactivity
Function / homology
Function and homology information


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 ...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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class Ib protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / T cell receptor complex / inner ear development / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / helical viral capsid / 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 / 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 / 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 / iron ion transport / peptide antigen assembly with MHC class I protein complex / 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 / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / protein refolding / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 / viral nucleocapsid / 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 / host cell cytoplasm / early endosome / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / defense response to Gram-positive bacterium / immune response / receptor ligand activity / ribonucleoprotein complex / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / : / RNA binding
Similarity search - Function
: / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / : / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...: / Rhabdovirus nucleocapsid / Rhabdovirus nucleocapsid, N-terminal / Rhabdovirus nucleocapsid, C-terminal / Rhabdovirus nucleoprotein-like / Rhabdovirus nucleocapsid protein / : / 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/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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / 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 / Nucleoprotein / TRADV16D
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsReiser, J.-B. / Darnault, C. / Gregoire, C. / Mosser, T. / Mazza, G. / Kearnay, A. / van der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B.
Citation
Journal: Nat.Immunol. / Year: 2003
Title: CDR3 loop flexibility contributes to the degeneracy of TCR recognition
Authors: Reiser, J.-B. / Darnault, C. / Gregoire, C. / Mosser, T. / Mazza, G. / Kearnay, A. / van der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B.
#1: 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.
#2: 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.
#3: Journal: Science / Year: 1992
Title: Crystal Structures of Two Viral Peptides in Complex with Murine MHC Class I H-2Kb
Authors: Fremont, D.H. / Matsumura, M. / Stura, E.A. / Peterson, P.A. / Wilson, I.A.
History
DepositionNov 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / Database references / 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_ref_seq_dif / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Author states the sequence of the BM3.3 TCR has never been deposited in any database, ...SEQUENCE Author states the sequence of the BM3.3 TCR has never been deposited in any database, however it has been published in the following paper: Couez D, Malissen M, Buferne M, Schmitt-Verhulst AM, Malissen B. (1991) Each of the two productive T cell receptor alpha-gene rearrangements found in both the A10 and BM 3.3 T cell clones give rise to an alpha chain which can contribute to the constitution of a surface-expressed alpha beta dimer. Int Immunol. 3(7):719-29. Moreover, TCR sequences are the result of V,J and C genes recombination for the alpha chain, V, D, J, C genes recombination for the beta chain. The BM3.3 TCR variable domain is made of the following segments: TRAV16*01, TRAJ32 for the Valpha and Jalpha segments (chain A) TRBV1*01, TRBJ1-3*01 for the Vbeta, Jbeta segments (chain B). Author states the TCR variable domain is produced as a single chain Fv fragment. The Valpha domain (chain A) C-terminus is artificially connected to the Vbeta domain (chain B) N-terminus by the mean of a flexible hydrophilic linker (sequence GSADDASADDAKKDAAKKDDAKKDDAKKDGS) for wich no electron density is observed. Since this linker has no biological role and does not interfere with TCR recognition, it has not been incorporated in the model and the sequence record.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BM3.3 T Cell Receptor alpha-Chain
B: BM3.3 T Cell Receptor beta-Chain
H: H-2 class I histocompatibility antigen, K-B alpha chain precursor
P: Nucleocapsid
L: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0046
Polymers70,5805
Non-polymers4241
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-17 kcal/mol
Surface area29280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.860, 101.860, 201.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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BM3.3 T Cell Receptor ... , 2 types, 2 molecules AB

#1: 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: UniProt: Q5R1F1*PLUS
#2: Protein BM3.3 T Cell Receptor beta-Chain


Mass: 13064.964 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: UniProt: P04214*PLUS

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Protein , 2 types, 2 molecules HL

#3: Protein H-2 class I histocompatibility antigen, K-B alpha chain precursor / H-2KB


Mass: 31777.438 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) / Gene: H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#5: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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Protein/peptide / Sugars / Non-polymers , 3 types, 103 molecules P

#4: Protein/peptide Nucleocapsid / Nucleoprotein


Mass: 956.078 Da / Num. of mol.: 1
Fragment: Vesicular Stomatitis Virus Nucleoprotein fragment, residues (52-59)
Source method: obtained synthetically
Details: The 8-residue peptide of vesicular stomatitis virus was chemically synthesized.
References: UniProt: P11212
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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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: 3.66 Å3/Da / Density % sol: 66.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG6000 13-17%, MgAc 0.1M, NaCl 0-0.1M, Hepes 0.1M, pH 7.0 to 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
PH range low: 7.5 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)Chemical formula
14 mg/mlprotein1drop
213-17 %PEG60001reservoir
30.1 MHEPES1reservoirpH7.0-7.5
40-0.1 Mmagnesium acetate1reservoir
50-0.1 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→35.1 Å / Num. all: 29887 / Num. obs: 29887 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 60.2 Å2 / Rsym value: 0.083 / Net I/σ(I): 7.9
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2033 / Rsym value: 0.437 / % possible all: 99.2
Reflection
*PLUS
Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.437

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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: PDB ENTRY 1FO0

1fo0


Resolution: 2.7→12 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29767 2879 -Random
Rwork0.23049 ---
all0.23741 25666 --
obs0.23741 25666 96.51 %-
Displacement parametersBiso mean: 56.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2--1.68 Å20 Å2
3----3.36 Å2
Refinement stepCycle: LAST / Resolution: 2.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4962 0 28 101 5091
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.021
X-RAY DIFFRACTIONp_angle_d1.2741.947
LS refinement shellResolution: 2.7→2.79 Å
RfactorNum. reflection
Rfree0.406 253
Rwork0.331 -
obs-2433
Refinement
*PLUS
Rfactor obs: 0.237 / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.271.947

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