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- PDB-2icw: Crystal structure of a complete ternary complex between TCR, supe... -

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Basic information

Entry
Database: PDB / ID: 2icw
TitleCrystal structure of a complete ternary complex between TCR, superantigen, and peptide-MHC class II molecule
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • (T-cell receptor ...) x 2
  • Mycoplasma arthritidis mitogen
  • haemagglutinin peptide
KeywordsIMMUNE SYSTEM / TCR / MHC / superantigen / protein-protein complex
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / intermediate filament / T-helper 1 type immune response / T cell receptor complex / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / cognition / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / positive regulation of protein phosphorylation / early endosome membrane / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / lysosome / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
mam-mhc complex, Chain D, Domain 2 / Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1 / Mycoplasma arthritidis-derived mitogen / Superantigen MAM / Mycoplasma arthritidis-derived mitogen, C-terminal / Mycoplasma arthritidis-derived mitogen / : / : / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 ...mam-mhc complex, Chain D, Domain 2 / Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1 / Mycoplasma arthritidis-derived mitogen / Superantigen MAM / Mycoplasma arthritidis-derived mitogen, C-terminal / Mycoplasma arthritidis-derived mitogen / : / : / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Arc Repressor Mutant, subunit A / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Beta-chain / T-cell receptor alpha chain V region PHDS58 / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / T-cell receptor beta chain V region C5 / HLA class II histocompatibility antigen, DRB1 beta chain / Superantigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycoplasma arthritidis (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsWang, L. / Zhao, Y. / Li, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Crystal structure of a complete ternary complex of TCR, superantigen and peptide-MHC.
Authors: Wang, L. / Zhao, Y. / Li, Z. / Guo, Y. / Jones, L.L. / Kranz, D.M. / Mourad, W. / Li, H.
History
DepositionSep 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequence of chains J and L are consistent with the sequence of chain B in the PDB entry 1TCR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: haemagglutinin peptide
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: haemagglutinin peptide
G: Mycoplasma arthritidis mitogen
H: Mycoplasma arthritidis mitogen
I: T-cell receptor alpha chain V
J: T-cell receptor beta chain V
K: T-cell receptor alpha chain V
L: T-cell receptor beta chain V


Theoretical massNumber of molelcules
Total (without water)188,40212
Polymers188,40212
Non-polymers00
Water5,495305
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: haemagglutinin peptide
G: Mycoplasma arthritidis mitogen
I: T-cell receptor alpha chain V
J: T-cell receptor beta chain V


Theoretical massNumber of molelcules
Total (without water)94,2016
Polymers94,2016
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: haemagglutinin peptide
H: Mycoplasma arthritidis mitogen
K: T-cell receptor alpha chain V
L: T-cell receptor beta chain V


Theoretical massNumber of molelcules
Total (without water)94,2016
Polymers94,2016
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.516, 86.822, 116.981
Angle α, β, γ (deg.)110.270, 92.320, 107.870
Int Tables number1
Space group name H-MP1

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Components

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HLA class II histocompatibility antigen, ... , 2 types, 4 molecules ADBE

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 20983.176 Da / Num. of mol.: 2 / Fragment: residues 28-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 22080.664 Da / Num. of mol.: 2 / Fragment: residues 30-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P04229, UniProt: P01911*PLUS

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T-cell receptor ... , 2 types, 4 molecules IKJL

#5: Protein T-cell receptor alpha chain V


Mass: 12113.593 Da / Num. of mol.: 2 / Fragment: residues 21-131 / Mutation: W82R, L43P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01738
#6: Protein T-cell receptor beta chain V


Mass: 12184.312 Da / Num. of mol.: 2 / Mutation: G17E, G42E, L80S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04213, UniProt: A2NTY6*PLUS

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Protein/peptide / Protein / Non-polymers , 3 types, 309 molecules CFGH

#3: Protein/peptide haemagglutinin peptide


Mass: 1506.807 Da / Num. of mol.: 2 / Fragment: residues 306-318 / Source method: obtained synthetically / Details: This sequence occurs naturally in Influenza virus
#4: Protein Mycoplasma arthritidis mitogen


Mass: 25332.328 Da / Num. of mol.: 2 / Fragment: residues 26-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma arthritidis (bacteria) / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q48898
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.91 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.6
Details: 13-15% PEG 4000, 5% isopropanol, 0.1 M sodium citrate, 2 mM zinc acetate, pH 5.6, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.4→47.8 Å / Num. all: 78311 / Num. obs: 78311 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 16.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.7 / Num. unique all: 7476 / Rsym value: 0.58 / % possible all: 91.6

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Processing

Software
NameVersionClassificationNB
CNS1refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R5I, 1TCR

1r5i

1tcr


Resolution: 2.41→47.79 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2277677.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.288 3944 5 %RANDOM
Rwork0.242 ---
all0.242 78311 --
obs0.242 78299 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.051 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 62.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.39 Å215.09 Å23.87 Å2
2---2.66 Å22.67 Å2
3----7.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.41→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13159 0 0 305 13464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.424 546 4.9 %
Rwork0.389 10650 -
obs-11196 80.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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