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- PDB-7z50: Structure of the highly diabetogenic 4.1-T cell receptor targetin... -

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Basic information

Entry
Database: PDB / ID: 7z50
TitleStructure of the highly diabetogenic 4.1-T cell receptor targeting a hybrid insulin peptide bound to I-Ag7.
Components
  • 4.1 TCR alpha chain
  • 4.1 TCR beta chain
  • H-2 class II histocompatibility antigen, A-D alpha chain
  • H2-Ab1 protein
  • Hybrid insulin peptide
KeywordsIMMUNE SYSTEM / Diabetes / T cell receptor / murine MHC class II / hybrid insulin peptide
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
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 ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly 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 / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLopez-Sagaseta, J. / Erausquin, E.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessRTI2018-093964-B-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2017-21683 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-094894-B-I00 Spain
CitationJournal: Front Immunol / Year: 2022
Title: Structural plasticity in I-A g7 links autoreactivity to hybrid insulin peptides in type I diabetes.
Authors: Erausquin, E. / Serra, P. / Parras, D. / Santamaria, P. / Lopez-Sagaseta, J.
History
DepositionMar 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 17, 2022Group: Database references / Category: citation_author
Revision 1.3Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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, A-D alpha chain
B: H2-Ab1 protein
C: H-2 class II histocompatibility antigen, A-D alpha chain
D: H2-Ab1 protein
E: 4.1 TCR beta chain
F: 4.1 TCR beta chain
G: 4.1 TCR alpha chain
H: 4.1 TCR alpha chain
T: Hybrid insulin peptide
W: Hybrid insulin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,26524
Polymers202,70610
Non-polymers1,56014
Water5,999333
1
A: H-2 class II histocompatibility antigen, A-D alpha chain
B: H2-Ab1 protein
E: 4.1 TCR beta chain
H: 4.1 TCR alpha chain
T: Hybrid insulin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,00411
Polymers101,3535
Non-polymers6526
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: H-2 class II histocompatibility antigen, A-D alpha chain
D: H2-Ab1 protein
F: 4.1 TCR beta chain
G: 4.1 TCR alpha chain
W: Hybrid insulin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,26113
Polymers101,3535
Non-polymers9088
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.615, 133.457, 102.560
Angle α, β, γ (deg.)90.000, 103.690, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11F-301-

NA

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 10 or (resid 11...
d_2ens_1(chain "C" and (resid 2 through 38 or (resid 39...
d_1ens_2(chain "B" and (resid 5 through 100 or (resid 101...
d_2ens_2(chain "D" and (resid 5 through 58 or (resid 59...
d_1ens_3(chain "E" and ((resid 1 and (name N or name...
d_2ens_3(chain "F" and (resid 1 through 9 or (resid 10...
d_1ens_4(chain "G" and (resid 4 through 5 or (resid 6...
d_2ens_4(chain "H" and (resid 4 through 68 or (resid 69...
d_1ens_5chain "T"
d_2ens_5(chain "W" and resid -1 through 11)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ILEPROA2 - 182
d_21ens_1ILEPROC1 - 181
d_11ens_2ARGPROB1 - 152
d_12ens_2GLYTRPB155 - 175
d_21ens_2ARGTRPD1 - 173
d_11ens_3METALAE1 - 241
d_21ens_3METALAF1 - 241
d_11ens_4GLNSERG1 - 144
d_12ens_4ASPASNG146 - 185
d_21ens_4GLNSERI1 - 144
d_22ens_4ASPASNI146 - 185
d_11ens_5LEUCYSU1 - 13
d_21ens_5LEUCYSV1 - 13

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(0.891632297634, -0.0135474608177, 0.452557523549), (-0.0131161910307, -0.999905610626, -0.00409088887066), (0.452570228084, -0.00228826228813, -0.891725828104)-6.32098675714, -14.2332300639, 25.6095705484
2given(0.893103230579, -0.00200204830913, 0.449847320023), (0.00477538076073, -0.999891558205, -0.0139308136542), (0.449826427934, 0.0145898469164, -0.892996820318)-6.43799985681, -14.5048163995, 25.536037623
3given(0.900968211691, -0.0393595428878, 0.432096178999), (-0.0316035590435, -0.999184802992, -0.0251186091414), (0.432732592461, 0.00897529125285, -0.901477646739)-5.76023197701, -12.6504120519, 26.9011578252
4given(0.897609917481, -0.0225513643566, 0.440213439148), (-0.0320714887819, -0.99938472741, 0.0141981064703), (0.439622401213, -0.0268626615525, -0.897780898531)-6.47839763624, -13.73037835, 25.4494575033
5given(0.892019868765, -0.0160323392083, 0.451711764102), (-0.0151777461797, -0.999869599368, -0.00551545836047), (0.451741286302, -0.00193606805901, -0.892146883585)-6.29614232754, -14.0776481407, 25.6724125374

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Components

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Protein , 4 types, 8 molecules ACBDEFGH

#1: Protein H-2 class II histocompatibility antigen, A-D alpha chain


Mass: 23027.711 Da / Num. of mol.: 2 / Mutation: I91C
Source method: isolated from a genetically manipulated source
Details: This polypeptide corresponds to the alpha chain of a murine major histocompatibility complex (MHC) class II molecule.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P04228
#2: Protein H2-Ab1 protein


Mass: 26263.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Hybrid insulin peptide covalently bound through glycine-serine linker to N-terminal of polypeptide. This polypeptide corresponds to the alpha chain of a murine major histocompatibility ...Details: Hybrid insulin peptide covalently bound through glycine-serine linker to N-terminal of polypeptide. This polypeptide corresponds to the alpha chain of a murine major histocompatibility complex (MHC) class II molecule.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1 / Cell line (production host): CHO-S / Organ (production host): Ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q31135
#3: Protein 4.1 TCR beta chain


Mass: 27323.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Protein 4.1 TCR alpha chain


Mass: 23178.820 Da / Num. of mol.: 2
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, 7 molecules TW

#5: Protein/peptide Hybrid insulin peptide


Mass: 1559.694 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal G-G residues from the G-S linker / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#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.: 5 / Source method: obtained synthetically / 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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Non-polymers , 4 types, 342 molecules

#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.32 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M MgCl2, 0.1 M Na HEPES pH 7.0, 15% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2021
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.65→49.82 Å / Num. obs: 81036 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 58.56 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.107 / Rrim(I) all: 0.169 / Χ2: 0.97 / Net I/σ(I): 8.1
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.254 / Mean I/σ(I) obs: 1 / Num. unique obs: 4458 / CC1/2: 0.371 / Χ2: 0.98 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSBUILT=20210205data reduction
Aimless1.12.8data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QHP

7qhp


Resolution: 2.65→49.82 Å / SU ML: 0.3927 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2611 4063 5.02 %
Rwork0.2212 76946 -
obs0.2232 81009 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.89 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12286 0 97 333 12716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212690
X-RAY DIFFRACTIONf_angle_d0.493117311
X-RAY DIFFRACTIONf_chiral_restr0.0441933
X-RAY DIFFRACTIONf_plane_restr0.00432253
X-RAY DIFFRACTIONf_dihedral_angle_d5.98931753
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.3306105313
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.580804004595
ens_3d_2EX-RAY DIFFRACTIONTorsion NCS0.655102401987
ens_4d_2GX-RAY DIFFRACTIONTorsion NCS0.931089138913
ens_5d_2TX-RAY DIFFRACTIONTorsion NCS0.260487561943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.680.36931480.32592638X-RAY DIFFRACTION99.75
2.68-2.710.33991370.31672632X-RAY DIFFRACTION99.71
2.71-2.750.37421420.30572646X-RAY DIFFRACTION99.89
2.75-2.780.33691300.30192652X-RAY DIFFRACTION100
2.78-2.820.34681420.30532625X-RAY DIFFRACTION99.96
2.82-2.860.35271280.29112706X-RAY DIFFRACTION100
2.86-2.910.31281430.28932641X-RAY DIFFRACTION99.86
2.91-2.950.31771480.28842603X-RAY DIFFRACTION99.93
2.95-30.33841320.27462656X-RAY DIFFRACTION99.93
3-3.050.31431510.27052629X-RAY DIFFRACTION99.86
3.05-3.110.32151480.25542661X-RAY DIFFRACTION99.89
3.11-3.170.29561300.24232639X-RAY DIFFRACTION99.93
3.17-3.230.28261390.23772669X-RAY DIFFRACTION99.93
3.23-3.30.26281480.22862631X-RAY DIFFRACTION99.93
3.3-3.380.27631390.22862620X-RAY DIFFRACTION99.96
3.38-3.460.28121230.22752676X-RAY DIFFRACTION99.93
3.46-3.560.26551470.20812647X-RAY DIFFRACTION99.82
3.56-3.660.29471390.21832642X-RAY DIFFRACTION99.75
3.66-3.780.24431450.20282642X-RAY DIFFRACTION99.82
3.78-3.910.21531220.2012681X-RAY DIFFRACTION99.86
3.91-4.070.25811380.20462654X-RAY DIFFRACTION99.86
4.07-4.260.22571440.20232631X-RAY DIFFRACTION99.75
4.26-4.480.20411410.17892670X-RAY DIFFRACTION99.89
4.48-4.760.20891400.16692654X-RAY DIFFRACTION99.68
4.76-5.130.23481460.18452644X-RAY DIFFRACTION99.68
5.13-5.640.22851370.19932677X-RAY DIFFRACTION99.86
5.64-6.460.25971510.2322671X-RAY DIFFRACTION99.89
6.46-8.130.26961460.23122684X-RAY DIFFRACTION99.89
8.13-49.820.25271390.22632725X-RAY DIFFRACTION99.51
Refinement TLS params.Method: refined / Origin x: 53.3836749293 Å / Origin y: -7.60753405718 Å / Origin z: 26.3685136101 Å
111213212223313233
T0.35388961664 Å2-0.0218185632939 Å2-0.0104675681335 Å2-0.388572999431 Å20.00196702800324 Å2--0.324072383745 Å2
L0.0772055775979 °20.0121656197754 °2-0.071702296402 °2-0.408819574329 °2-0.000925294832821 °2--0.162715494234 °2
S0.0265970179269 Å °-0.0457717423518 Å °0.0211127995237 Å °0.0180869535545 Å °-0.038648525375 Å °-0.0605408584468 Å °-0.0194020491679 Å °0.106933585214 Å °0.0147457181634 Å °
Refinement TLS groupSelection details: all

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