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- PDB-3qiw: Crystal structure of the 226 TCR in complex with MCC-p5E/I-Ek -

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Basic information

Entry
Database: PDB / ID: 3qiw
TitleCrystal structure of the 226 TCR in complex with MCC-p5E/I-Ek
Components
  • H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K alpha chain
  • MCC-p5E peptide
  • MHC CLASS II H2-IA-BETA CHAIN
  • TCR 226 alpha chain
  • TCR 226 beta chain
KeywordsIMMUNE SYSTEM / immunoglobulin domain / T cell receptor / MHC molecule
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / MHC class II antigen presentation / immunoglobulin mediated immune response / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / MHC class II antigen presentation / immunoglobulin mediated immune response / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / mitochondrial intermembrane space / MHC class II protein complex binding / late endosome membrane / adaptive immune response / electron transfer activity / lysosome / lysosomal membrane / external side of plasma membrane / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Cytochrome c, class IA/ IB / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Cytochrome c, class IA/ IB / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cytochrome c / H-2 class II histocompatibility antigen, E-K alpha chain / H-2 class II histocompatibility antigen, E-B beta chain / MHC class II antigen IEk-beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Manduca sexta (tobacco hornworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsKruse, A.C. / Ely, L.K. / Newell, E.W. / Davis, M.M. / Garcia, K.C.
CitationJournal: J.Immunol. / Year: 2011
Title: Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k).
Authors: Newell, E.W. / Ely, L.K. / Kruse, A.C. / Reay, P.A. / Rodriguez, S.N. / Lin, A.E. / Kuhns, M.S. / Garcia, K.C. / Davis, M.M.
History
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 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 1.5Oct 16, 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
A: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K alpha chain
B: MHC CLASS II H2-IA-BETA CHAIN
C: TCR 226 alpha chain
D: TCR 226 beta chain
E: MCC-p5E peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6067
Polymers97,1635
Non-polymers4422
Water00
1
C: TCR 226 alpha chain

D: TCR 226 beta chain

A: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K alpha chain
B: MHC CLASS II H2-IA-BETA CHAIN
E: MCC-p5E peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6067
Polymers97,1635
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_545-x,y-1/2,-z1
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-41 kcal/mol
Surface area39400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.179, 71.624, 105.659
Angle α, β, γ (deg.)90.00, 90.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K alpha chain


Mass: 22361.051 Da / Num. of mol.: 1 / Fragment: unp residues 26-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04224
#2: Protein MHC CLASS II H2-IA-BETA CHAIN


Mass: 22972.594 Da / Num. of mol.: 1 / Fragment: unp residues 29-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Eb1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31163, UniProt: P04230*PLUS
#3: Protein TCR 226 alpha chain


Mass: 22822.301 Da / Num. of mol.: 1 / Fragment: unp residues 97-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Production host: Escherichia coli (E. coli)
#4: Protein TCR 226 beta chain


Mass: 27613.924 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)

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Protein/peptide / Sugars , 2 types, 3 molecules E

#5: Protein/peptide MCC-p5E peptide


Mass: 1393.562 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: P00039
#6: 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: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 295 K / pH: 6.5
Details: 15-20% PEG5000 MME, Bis tris, VAPOR DIFFUSION, temperature 295K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→45 Å / Num. obs: 16259 / % possible obs: 98.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.9
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.345 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3QIU

3qiu


Resolution: 3.3→36.69 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.44 / σ(F): 1.36 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 835 5.14 %
Rwork0.212 --
obs0.215 16244 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.48 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 62.75 Å2
Baniso -1Baniso -2Baniso -3
1-27.419 Å2-0 Å20.991 Å2
2---7.6606 Å20 Å2
3----22.1096 Å2
Refinement stepCycle: LAST / Resolution: 3.3→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6230 0 28 0 6258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086422
X-RAY DIFFRACTIONf_angle_d0.7578696
X-RAY DIFFRACTIONf_dihedral_angle_d14.6592314
X-RAY DIFFRACTIONf_chiral_restr0.046942
X-RAY DIFFRACTIONf_plane_restr0.0031133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2953-3.50160.39631340.2912563X-RAY DIFFRACTION99
3.5016-3.77170.30231440.24962572X-RAY DIFFRACTION99
3.7717-4.15080.28371250.20342535X-RAY DIFFRACTION99
4.1508-4.75030.21041390.17312588X-RAY DIFFRACTION98
4.7503-5.98070.24251460.18432565X-RAY DIFFRACTION98
5.9807-36.6950.23711470.20622586X-RAY DIFFRACTION97

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