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- PDB-3mbe: TCR 21.30 in complex with MHC class II I-Ag7HEL(11-27) -

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Basic information

Entry
Database: PDB / ID: 3mbe
TitleTCR 21.30 in complex with MHC class II I-Ag7HEL(11-27)
Components
  • (MHC CLASS II H2-IAg7 ...) x 2
  • PEPTIDE HEL 11-27
  • TCR 21.3 alpha chain
  • TCR 21.3 beta chain
KeywordsIMMUNE SYSTEM / T cell receptor / Histocompatability antigen / MHC class II / I-Ag7
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / alpha-beta T cell receptor complex / positive regulation of T cell differentiation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / alpha-beta T cell receptor complex / positive regulation of T cell differentiation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / response to bacterium / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / cell wall macromolecule catabolic process / signaling receptor activity / lysozyme / MHC class II protein complex binding / late endosome membrane / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / adaptive immune response / lysosome / early endosome / defense response to Gram-positive bacterium / defense response to bacterium / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / 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 ...T-cell receptor alpha chain, constant domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Domain of unknown function (DUF1968) / 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 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / MHC classes I/II-like antigen recognition protein / Lysozyme-like domain superfamily / 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
Lysozyme C / T-cell receptor alpha chain constant / T-cell receptor beta-1 chain C region / H-2 class II histocompatibility antigen, A-D alpha chain / H2-Ab1 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.886 Å
AuthorsCorper, A.L. / Yoshida, K. / Teyton, L. / Wilson, I.A.
CitationJournal: J.Clin.Invest. / Year: 2010
Title: The diabetogenic mouse MHC class II molecule I-Ag7 is endowed with a switch that modulates TCR affinity.
Authors: Yoshida, K. / Corper, A.L. / Herro, R. / Jabri, B. / Wilson, I.A. / Teyton, L.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 10, 2013Group: Structure summary
Revision 1.3May 15, 2013Group: Database references / Source and taxonomy
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC CLASS II H2-IAg7 ALPHA CHAIN
B: MHC CLASS II H2-IAg7 BETA CHAIN
P: PEPTIDE HEL 11-27
C: TCR 21.3 alpha chain
D: TCR 21.3 beta chain
E: MHC CLASS II H2-IAg7 ALPHA CHAIN
F: MHC CLASS II H2-IAg7 BETA CHAIN
Q: PEPTIDE HEL 11-27
G: TCR 21.3 alpha chain
H: TCR 21.3 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,93114
Polymers202,63910
Non-polymers1,2914
Water0
1
A: MHC CLASS II H2-IAg7 ALPHA CHAIN
B: MHC CLASS II H2-IAg7 BETA CHAIN
P: PEPTIDE HEL 11-27
C: TCR 21.3 alpha chain
D: TCR 21.3 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9657
Polymers101,3205
Non-polymers6462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: MHC CLASS II H2-IAg7 ALPHA CHAIN
F: MHC CLASS II H2-IAg7 BETA CHAIN
Q: PEPTIDE HEL 11-27
G: TCR 21.3 alpha chain
H: TCR 21.3 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9657
Polymers101,3205
Non-polymers6462
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.468, 99.391, 404.677
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21H
12C
22G
13A
23E
14B
24F
15P
25Q
16A
26E
17D
27H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain D and (resseq 3:252 )D3 - 252
211chain H and (resseq 3:252 )H3 - 252
112chain C and (resseq 2:211 )C2 - 211
212chain G and (resseq 2:211 )G2 - 211
113chain A and (resseq 1B:182 )A1
213chain E and (resseq 1B:182 )E1
114chain B and (resseq 5:105 or resseq 112:189 )B5 - 105
124chain B and (resseq 5:105 or resseq 112:189 )B112 - 189
214chain F and (resseq 5:105 or resseq 112:189 )F5 - 105
224chain F and (resseq 5:105 or resseq 112:189 )F112 - 189
115chain P and (resseq 10:26 )P10 - 26
215chain Q and (resseq 10:26 )Q10 - 26
116chain A and (resseq 300 )A300
216chain E and (resseq 300 )E300
117chain D and (resseq 300:301 )D300 - 301
217chain H and (resseq 300:301 )H300 - 301

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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MHC CLASS II H2-IAg7 ... , 2 types, 4 molecules AEBF

#1: Protein MHC CLASS II H2-IAg7 ALPHA CHAIN / H-2 class II histocompatibility antigen / A-D alpha chain


Mass: 21623.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Plasmid: pRMHa-3 / Production host: Drosophila Melanogaster (fruit fly) / Strain (production host): S2 cells / References: UniProt: P04228
#2: Protein MHC CLASS II H2-IAg7 BETA CHAIN / MHC class II H2-IA-beta chain (haplotype NOD)


Mass: 23341.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1 / Plasmid: pRMHa-3 / Production host: Drosophila Melanogaster (fruit fly) / Strain (production host): S2 cells / References: UniProt: Q31135

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Protein/peptide , 1 types, 2 molecules PQ

#3: Protein/peptide PEPTIDE HEL 11-27


Mass: 2013.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P00698

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Protein , 2 types, 4 molecules CGDH

#4: Protein TCR 21.3 alpha chain


Mass: 25391.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1 / Plasmid: pRMHa-3 / Production host: Drosophila Melanogaster (fruit fly) / Strain (production host): S2 cells / References: UniProt: P01849*PLUS
#5: Protein TCR 21.3 beta chain


Mass: 28950.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1 / Plasmid: pRMHa-3 / Production host: Drosophila Melanogaster (fruit fly) / Strain (production host): S2 cells / References: UniProt: P01852*PLUS

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Sugars , 2 types, 4 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: 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 / N-Acetylglucosamine


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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG4000, 0.2M K formate, 0.1M Na Cacodylate., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.07229 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2009
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07229 Å / Relative weight: 1
ReflectionResolution: 2.88→48.26 Å / Num. all: 63068 / Num. obs: 43435 / % possible obs: 68.9 % / Observed criterion σ(I): -3 / Redundancy: 1.99 % / Biso Wilson estimate: 42.69 Å2 / Rsym value: 0.1121
Reflection shellResolution: 2.88→2.98 Å / Redundancy: 0.35 % / Mean I/σ(I) obs: 0.98 / Num. unique all: 6028 / Rsym value: 0.4319 / % possible all: 26.4

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Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
XPREPdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: I-Ag7GPI282-292 (unpublished), PDB ENTRY 1MWA

1mwa


Resolution: 2.886→48.261 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.281 727 2.13 %RANDOM
Rwork0.253 ---
obs0.254 34208 54.66 %-
all-63068 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.937 Å2 / ksol: 0.294 e/Å3
Displacement parametersBiso max: 193.57 Å2 / Biso mean: 71.833 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1--4.565 Å2-0 Å20 Å2
2---2.063 Å20 Å2
3---6.628 Å2
Refinement stepCycle: LAST / Resolution: 2.886→48.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12944 0 84 0 13028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713382
X-RAY DIFFRACTIONf_angle_d1.00218144
X-RAY DIFFRACTIONf_chiral_restr0.0651954
X-RAY DIFFRACTIONf_plane_restr0.0042350
X-RAY DIFFRACTIONf_dihedral_angle_d21.0664804
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D1878X-RAY DIFFRACTIONPOSITIONAL0.022
12H1878X-RAY DIFFRACTIONPOSITIONAL0.022
21C1494X-RAY DIFFRACTIONPOSITIONAL0.018
22G1494X-RAY DIFFRACTIONPOSITIONAL0.018
31A1481X-RAY DIFFRACTIONPOSITIONAL0.02
32E1481X-RAY DIFFRACTIONPOSITIONAL0.02
41B1487X-RAY DIFFRACTIONPOSITIONAL0.02
42F1487X-RAY DIFFRACTIONPOSITIONAL0.02
51P132X-RAY DIFFRACTIONPOSITIONAL0.02
52Q132X-RAY DIFFRACTIONPOSITIONAL0.02
61A14X-RAY DIFFRACTIONPOSITIONAL0.013
62E14X-RAY DIFFRACTIONPOSITIONAL0.013
71D28X-RAY DIFFRACTIONPOSITIONAL0.015
72H28X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.886-3.1080.421100.3736706806806
3.108-3.4210.382620.3223142376237619
3.421-3.9160.2911420.29260356177617750
3.916-4.9330.2722380.23711762120001200096
4.933-48.2680.2682750.24127001297512975100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75410.0609-0.10790.64590.41680.85480.0188-0.1786-0.03-0.54460.2125-0.4077-0.25860.51260.45460.0640.006-0.1502-0.12490.0922-0.0084-21.66821.2281-66.3658
20.6022-0.2473-0.5350.46390.07790.38620.2642-0.48130.0547-0.675-0.33320.1163-0.5568-0.0518-0.03160.5350.00890.15430.8939-0.00750.125511.8723-45.5821-30.4933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A or chain B or chain C or chain D or chain PA1 - 300
2X-RAY DIFFRACTION1chain A or chain B or chain C or chain D or chain PB5 - 189
3X-RAY DIFFRACTION1chain A or chain B or chain C or chain D or chain PC2 - 211
4X-RAY DIFFRACTION1chain A or chain B or chain C or chain D or chain PD3 - 301
5X-RAY DIFFRACTION1chain A or chain B or chain C or chain D or chain PP10 - 26
6X-RAY DIFFRACTION2chain E or chain F or chain G or chain H or chain QE1 - 300
7X-RAY DIFFRACTION2chain E or chain F or chain G or chain H or chain QF5 - 189
8X-RAY DIFFRACTION2chain E or chain F or chain G or chain H or chain QG2 - 211
9X-RAY DIFFRACTION2chain E or chain F or chain G or chain H or chain QH3 - 301
10X-RAY DIFFRACTION2chain E or chain F or chain G or chain H or chain QQ10 - 26

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