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- PDB-1u3h: Crystal structure of mouse TCR 172.10 complexed with MHC class II... -

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Basic information

Entry
Database: PDB / ID: 1u3h
TitleCrystal structure of mouse TCR 172.10 complexed with MHC class II I-Au molecule at 2.4 A
Components
  • (H-2 class II histocompatibility antigen, A-U ...) x 2
  • Mouse TCRVbeta 172.10, extracellular variable domain
  • Myelin basic protein (MBP)-peptide
  • T-cell receptor alpha-chain
KeywordsIMMUNE SYSTEM / complex
Function / homology
Function and homology information


compact myelin / structural constituent of myelin sheath / internode region of axon / negative regulation of axonogenesis / negative regulation of heterotypic cell-cell adhesion / antigen processing and presentation of peptide antigen / membrane organization / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of T cell differentiation / T cell receptor complex ...compact myelin / structural constituent of myelin sheath / internode region of axon / negative regulation of axonogenesis / negative regulation of heterotypic cell-cell adhesion / antigen processing and presentation of peptide antigen / membrane organization / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of T cell differentiation / T cell receptor complex / maintenance of blood-brain barrier / antigen processing and presentation / negative regulation of T cell proliferation / myelination / multivesicular body / response to progesterone / cell projection / cell periphery / sensory perception of sound / response to toxic substance / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / positive regulation of interleukin-6 production / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MAPK cascade / positive regulation of T cell activation / myelin sheath / MHC class II protein complex binding / late endosome membrane / protease binding / adaptive immune response / lysosome / early endosome / cell surface receptor signaling pathway / calmodulin binding / lysosomal membrane / external side of plasma membrane / neuronal cell body / lipid binding / protein-containing complex binding / Golgi apparatus / cell surface / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Myelin basic protein / Myelin basic protein / Myelin basic protein signature. / 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 ...Myelin basic protein / Myelin basic protein / Myelin basic protein signature. / 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 / Immunoglobulin V-Type / 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 / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T-cell receptor beta chain V region C5 / Myelin basic protein / H-2 class II histocompatibility antigen, A-U beta chain / H-2 class II histocompatibility antigen, A-U alpha chain / TRAV14-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsMaynard, J. / Petersson, K. / Wilson, D.H. / Adams, E.J. / Blondelle, S.E. / Boulanger, M.J. / Wilson, D.B. / Garcia, K.C.
CitationJournal: Immunity / Year: 2005
Title: Structure of an autoimmune T cell receptor complexed with class II peptide-MHC: insights into MHC bias and antigen specificity
Authors: Maynard, J. / Petersson, K. / Wilson, D.H. / Adams, E.J. / Blondelle, S.E. / Boulanger, M.J. / Wilson, D.B. / Garcia, K.C.
History
DepositionJul 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2013Group: Other
Revision 1.4Feb 5, 2020Group: Database references / Derived calculations / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_struct_assembly ...pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.5Aug 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell receptor alpha-chain
B: Mouse TCRVbeta 172.10, extracellular variable domain
C: H-2 class II histocompatibility antigen, A-U alpha chain
D: H-2 class II histocompatibility antigen, A-U beta chain
P: Myelin basic protein (MBP)-peptide
E: T-cell receptor alpha-chain
F: Mouse TCRVbeta 172.10, extracellular variable domain
G: H-2 class II histocompatibility antigen, A-U alpha chain
H: H-2 class II histocompatibility antigen, A-U beta chain
I: Myelin basic protein (MBP)-peptide


Theoretical massNumber of molelcules
Total (without water)137,72710
Polymers137,72710
Non-polymers00
Water3,297183
1
A: T-cell receptor alpha-chain
B: Mouse TCRVbeta 172.10, extracellular variable domain
C: H-2 class II histocompatibility antigen, A-U alpha chain
D: H-2 class II histocompatibility antigen, A-U beta chain
P: Myelin basic protein (MBP)-peptide


Theoretical massNumber of molelcules
Total (without water)68,8635
Polymers68,8635
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: T-cell receptor alpha-chain
F: Mouse TCRVbeta 172.10, extracellular variable domain
G: H-2 class II histocompatibility antigen, A-U alpha chain
H: H-2 class II histocompatibility antigen, A-U beta chain
I: Myelin basic protein (MBP)-peptide


Theoretical massNumber of molelcules
Total (without water)68,8635
Polymers68,8635
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.835, 327.162, 127.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 4 molecules AEBF

#1: Protein T-cell receptor alpha-chain


Mass: 12290.634 Da / Num. of mol.: 2 / Fragment: V2.3-J39-C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pAK400 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5R1B3
#2: Protein Mouse TCRVbeta 172.10, extracellular variable domain


Mass: 12112.181 Da / Num. of mol.: 2 / Mutation: G17E,H47Y,I75T,L78S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pAK400 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04213

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H-2 class II histocompatibility antigen, A-U ... , 2 types, 4 molecules CGDH

#3: Protein H-2 class II histocompatibility antigen, A-U alpha chain


Mass: 20670.047 Da / Num. of mol.: 2 / Fragment: extracellular alpha-1, extracellular alpha-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Plasmid: pRMHa3 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14438
#4: Protein H-2 class II histocompatibility antigen, A-U beta chain


Mass: 22495.164 Da / Num. of mol.: 2 / Fragment: extracellular beta-1, extracellular beta-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRMHa3 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P06344

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Protein/peptide / Non-polymers , 2 types, 185 molecules PI

#5: Protein/peptide Myelin basic protein (MBP)-peptide


Mass: 1295.364 Da / Num. of mol.: 2 / Mutation: K4Y / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P04370*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.33 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 21% PEG 3350, 0.1M Hepes and 0.2M LiSO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 67849 / Num. obs: 67849 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 20.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6419 / Rsym value: 0.386 / % possible all: 93.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D9K

1d9k


Resolution: 2.42→41.51 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 195797.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3205 5.1 %RANDOM
Rwork0.232 ---
obs0.232 62711 89.1 %-
all-67849 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.9538 Å2 / ksol: 0.330412 e/Å3
Displacement parametersBiso mean: 61.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.12 Å20 Å20 Å2
2---23.09 Å20 Å2
3---28.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.42→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9726 0 0 183 9909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d1.07
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 364 5.1 %
Rwork0.387 6759 -
obs--60.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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