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- PDB-3qib: Crystal structure of the 2B4 TCR in complex with MCC/I-Ek -

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Basic information

Entry
Database: PDB / ID: 3qib
TitleCrystal structure of the 2B4 TCR in complex with MCC/I-Ek
Components
  • 2B4 beta chain
  • H-2 class II histocompatibility antigen, E-K alpha chain
  • MCC peptide
  • MHC class II E-beta-k
  • T-cell receptor alpha chain C region
KeywordsIMMUNE SYSTEM / Ig domain
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / MHC class II antigen presentation / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / immunoglobulin mediated immune response ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / MHC class II antigen presentation / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / immunoglobulin mediated immune response / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / response to bacterium / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / mitochondrial intermembrane space / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class II protein complex binding / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / electron transfer activity / lysosome / lysosomal membrane / external side of plasma membrane / heme binding / metal ion binding / plasma membrane
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) / Cytochrome c, class IA/ IB / 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 ...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) / Cytochrome c, class IA/ IB / 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 / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 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
beta-D-mannopyranose / alpha-L-fucopyranose / DI(HYDROXYETHYL)ETHER / Cytochrome c / T cell receptor alpha chain constant / H-2 class II histocompatibility antigen, E-K alpha chain / H-2 class II histocompatibility antigen, E-B beta chain / MHC class II antigen IEk-beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Manduca sexta (tobacco hornworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEly, L.K. / Newell, E.W. / Davis, M.M. / Garcia, K.C.
CitationJournal: J.Immunol. / Year: 2011
Title: Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k).
Authors: Newell, E.W. / Ely, L.K. / Kruse, A.C. / Reay, P.A. / Rodriguez, S.N. / Lin, A.E. / Kuhns, M.S. / Garcia, K.C. / Davis, M.M.
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq / struct_ref_seq_dif / 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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 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: H-2 class II histocompatibility antigen, E-K alpha chain
B: MHC class II E-beta-k
C: T-cell receptor alpha chain C region
D: 2B4 beta chain
P: MCC peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,02017
Polymers100,3265
Non-polymers1,69412
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17550 Å2
ΔGint-27 kcal/mol
Surface area34880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.749, 167.178, 259.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein H-2 class II histocompatibility antigen, E-K alpha chain


Mass: 22491.221 Da / Num. of mol.: 1 / Fragment: unp residues 26-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04224
#2: Protein MHC class II E-beta-k


Mass: 23344.934 Da / Num. of mol.: 1 / Fragment: unp residues 29-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Eb1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31163, UniProt: P04230*PLUS
#3: Protein T-cell receptor alpha chain C region


Mass: 22807.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCRA, TRAC / Production host: Escherichia coli (E. coli) / References: UniProt: P01848*PLUS
#4: Protein 2B4 beta chain


Mass: 30288.928 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)

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Protein/peptide , 1 types, 1 molecules P

#5: Protein/peptide MCC peptide


Mass: 1393.628 Da / Num. of mol.: 1 / Fragment: unp residues 97-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Production host: Escherichia coli (E. coli) / References: UniProt: P00039

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Sugars , 3 types, 5 molecules

#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.: 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
#7: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 113 molecules

#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.97 Å3/Da / Density % sol: 68.99 %
Crystal growTemperature: 295 K / pH: 6.2
Details: 50% PEG200, 0.2 M sodium chloride, 0.1 M sodium potassium phosphate, pH 6.2, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2009
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 43820

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.2_432) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→34.97 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 2192 5.04 %
Rwork0.221 --
obs0.222 43476 99.4 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.63 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4492 Å2-0 Å20 Å2
2---2.3339 Å2-0 Å2
3---3.7831 Å2
Refinement stepCycle: LAST / Resolution: 2.7→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6251 0 108 106 6465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016519
X-RAY DIFFRACTIONf_angle_d1.3048838
X-RAY DIFFRACTIONf_dihedral_angle_d15.4392340
X-RAY DIFFRACTIONf_chiral_restr0.085976
X-RAY DIFFRACTIONf_plane_restr0.0051147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.79650.33072200.31323910X-RAY DIFFRACTION96
2.7965-2.90840.30662160.27234097X-RAY DIFFRACTION99
2.9084-3.04070.27981900.2564128X-RAY DIFFRACTION100
3.0407-3.20090.28712190.24754102X-RAY DIFFRACTION100
3.2009-3.40130.28182280.23974121X-RAY DIFFRACTION100
3.4013-3.66370.25162120.22064153X-RAY DIFFRACTION100
3.6637-4.03190.23492240.2084137X-RAY DIFFRACTION100
4.0319-4.61420.22210.17574173X-RAY DIFFRACTION100
4.6142-5.80910.20352250.19074181X-RAY DIFFRACTION100
5.8091-34.9750.25062370.23424282X-RAY DIFFRACTION99

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