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- PDB-6dfs: mouse TCR I.29 in complex with IAg7-p8E9E6ss -

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Basic information

Entry
Database: PDB / ID: 6dfs
Titlemouse TCR I.29 in complex with IAg7-p8E9E6ss
Components
  • H-2 class II histocompatibility antigen, A-D alpha chain
  • H2-Ab1 protein
  • mouse TCR alpha chain
  • mouse TCR beta chain
KeywordsIMMUNE SYSTEM / T cell receptor / type 1 diabetes / autoimmunity
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / adaptive immune response / early endosome / lysosome ...antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / adaptive immune response / early endosome / lysosome / external side of plasma membrane / cell surface / Golgi apparatus / 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-D alpha chain / H2-Ab1 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsWang, Y. / Dai, S.
CitationJournal: Sci Immunol / Year: 2019
Title: How C-terminal additions to insulin B-chain fragments create superagonists for T cells in mouse and human type 1 diabetes.
Authors: Wang, Y. / Sosinowski, T. / Novikov, A. / Crawford, F. / White, J. / Jin, N. / Liu, Z. / Zou, J. / Neau, D. / Davidson, H.W. / Nakayama, M. / Kwok, W.W. / Gapin, L. / Marrack, P. / Kappler, J.W. / Dai, S.
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mouse TCR alpha chain
B: mouse TCR beta chain
C: H-2 class II histocompatibility antigen, A-D alpha chain
D: H2-Ab1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0085
Polymers96,7874
Non-polymers2211
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)269.518, 269.518, 45.639
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein mouse TCR alpha chain


Mass: 23361.896 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) / Strain (production host): BL21-Gold(DE3)pLysS AG
#2: Protein mouse TCR beta chain


Mass: 27747.234 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) / Strain (production host): BL21-Gold(DE3)pLysS AG
#3: Protein H-2 class II histocompatibility antigen, A-D alpha chain


Mass: 20896.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04228
#4: Protein H2-Ab1 protein


Mass: 24781.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31135

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Sugars / Non-polymers , 2 types, 20 molecules

#5: 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.: 1
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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.95 Å3/Da / Density % sol: 75.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 20000, 100mM bicine pH9.0, 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 32259 / % possible obs: 99.7 % / Redundancy: 6.3 % / Net I/σ(I): 24.4
Reflection shellResolution: 3.1→3.3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.1→50.01 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.841 / SU B: 21.205 / SU ML: 0.34 / Cross valid method: THROUGHOUT / ESU R: 0.713 / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28515 1713 5 %RANDOM
Rwork0.23964 ---
obs0.24197 32259 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20.23 Å20 Å2
2--0.47 Å2-0 Å2
3----1.52 Å2
Refinement stepCycle: 1 / Resolution: 3.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 0 14 19 6254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196409
X-RAY DIFFRACTIONr_bond_other_d0.0020.025814
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.9398724
X-RAY DIFFRACTIONr_angle_other_deg1.191313371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4195.032774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33524.164317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.918151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8171539
X-RAY DIFFRACTIONr_chiral_restr0.1130.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217290
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021543
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.1726.823112
X-RAY DIFFRACTIONr_mcbond_other6.1656.8183111
X-RAY DIFFRACTIONr_mcangle_it10.02410.1723876
X-RAY DIFFRACTIONr_mcangle_other10.02210.1743877
X-RAY DIFFRACTIONr_scbond_it5.3667.0983297
X-RAY DIFFRACTIONr_scbond_other5.3667.0983298
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.01610.534849
X-RAY DIFFRACTIONr_long_range_B_refined13.61253.2637140
X-RAY DIFFRACTIONr_long_range_B_other13.61253.2667141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 53 -
Rwork0.443 1403 -
obs--56.96 %

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