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- PDB-3rdt: Crystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/... -

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Basic information

Entry
Database: PDB / ID: 3rdt
TitleCrystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/3k peptide
Components
  • 3K peptide, linker and MHC H-2 class II I-Ab beta chain
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • TCR 809.B5 alpha chain
  • TCR 809.B5 beta chain
KeywordsIMMUNE SYSTEM / MHC / TCR / immune receptor / Ig-like domain
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / antigen processing and presentation / response to type II interferon / toxic substance binding ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / antigen processing and presentation / response to type II interferon / toxic substance binding / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / cellular response to type II interferon / adaptive immune response / early endosome / lysosome / immune response / external side of plasma membrane / ubiquitin protein ligase binding / Golgi apparatus / membrane / 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 / 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 / MHC classes I/II-like antigen recognition protein ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / 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
H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTrenh, P. / Huseby, E.S. / Stern, L.J.
CitationJournal: Immunity / Year: 2011
Title: A role for differential variable gene pairing in creating T cell receptors specific for unique major histocompatibility ligands.
Authors: Stadinski, B.D. / Trenh, P. / Smith, R.L. / Bautista, B. / Huseby, P.G. / Li, G. / Stern, L.J. / Huseby, E.S.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 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
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: 3K peptide, linker and MHC H-2 class II I-Ab beta chain
A: TCR 809.B5 alpha chain
B: TCR 809.B5 beta chain


Theoretical massNumber of molelcules
Total (without water)95,5974
Polymers95,5974
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)239.855, 73.016, 65.669
Angle α, β, γ (deg.)90.00, 90.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 20597.957 Da / Num. of mol.: 1 / Fragment: UNP residues 27-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14434
#2: Protein 3K peptide, linker and MHC H-2 class II I-Ab beta chain


Mass: 24966.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Mus musculus (house mouse)
Gene: H2-Ab1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14483
#3: Protein TCR 809.B5 alpha chain


Mass: 23029.490 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)
#4: Protein TCR 809.B5 beta chain


Mass: 27002.885 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)
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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 12% PEG 4000, 100mM sodium citrate, 100mM sodium cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2010 / Details: Monochromator, mirror
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 30664 / Num. obs: 30664 / % possible obs: 98.7 % / Redundancy: 4 % / Biso Wilson estimate: 45.74 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 18.6
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.77 / Rsym value: 0.54 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C60

3c60


Resolution: 2.7→30 Å / SU ML: 0.41 / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 1530 5 %
Rwork0.206 --
obs0.208 30618 98.4 %
all-30618 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.85 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1--6.2305 Å20 Å24.0373 Å2
2--21.9925 Å20 Å2
3----15.762 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 0 0 6399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086583
X-RAY DIFFRACTIONf_angle_d1.1028971
X-RAY DIFFRACTIONf_dihedral_angle_d15.0742309
X-RAY DIFFRACTIONf_chiral_restr0.078974
X-RAY DIFFRACTIONf_plane_restr0.0041175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80540.35951500.30022812X-RAY DIFFRACTION96
2.8054-2.91760.31011310.25512878X-RAY DIFFRACTION98
2.9176-3.05030.26511490.24552897X-RAY DIFFRACTION98
3.0503-3.21090.28641460.23172890X-RAY DIFFRACTION98
3.2109-3.41180.27041430.20792913X-RAY DIFFRACTION99
3.4118-3.67480.22541460.19352918X-RAY DIFFRACTION99
3.6748-4.04380.24961390.19682945X-RAY DIFFRACTION99
4.0438-4.62720.22371620.16982921X-RAY DIFFRACTION99
4.6272-5.82270.20151860.18372920X-RAY DIFFRACTION99
5.8227-29.98140.22911780.2152994X-RAY DIFFRACTION99

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