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- PDB-1fyt: CRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELL RECEP... -

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Basic information

Entry
Database: PDB / ID: 1fyt
TitleCRYSTAL STRUCTURE OF A COMPLEX OF A HUMAN ALPHA/BETA-T CELL RECEPTOR, INFLUENZA HA ANTIGEN PEPTIDE, AND MHC CLASS II MOLECULE, HLA-DR1
Components
  • (HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, ...) x 2
  • (T-CELL RECEPTOR ...) x 2
  • HEMAGGLUTININ HA1 PEPTIDE CHAIN
KeywordsIMMUNE SYSTEM / protein-protein complex / immunoglobulin fold
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 / alpha-beta T cell receptor complex / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / viral budding from plasma membrane / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / response to bacterium / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / host cell surface receptor binding / immune response / positive regulation of protein phosphorylation / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / Golgi membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / 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) / 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 / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / T cell receptor alpha chain constant / T cell receptor beta constant 1 / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Hemagglutinin / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
H3N2 subtype (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsHennecke, J. / Carfi, A. / Wiley, D.C.
CitationJournal: EMBO J. / Year: 2000
Title: Structure of a covalently stabilized complex of a human alphabeta T-cell receptor, influenza HA peptide and MHC class II molecule, HLA-DR1.
Authors: Hennecke, J. / Carfi, A. / Wiley, D.C.
History
DepositionOct 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Jul 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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, DR-1 BETA CHAIN
C: HEMAGGLUTININ HA1 PEPTIDE CHAIN
D: T-CELL RECEPTOR ALPHA CHAIN
E: T-CELL RECEPTOR BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7107
Polymers96,2685
Non-polymers4422
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.902, 73.439, 122.428
Angle α, β, γ (deg.)90.00, 108.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

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HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, ... , 2 types, 2 molecules AB

#1: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN / HLA-DR1 / DRA


Mass: 21084.826 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01903
#2: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-1 BETA CHAIN / HLA-DR1 / DRB1 0101


Mass: 22324.938 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04229, UniProt: P01911*PLUS

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T-CELL RECEPTOR ... , 2 types, 2 molecules DE

#4: Protein T-CELL RECEPTOR ALPHA CHAIN / TCR HA1.7 ALPHA CHAIN


Mass: 23408.016 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: PIR: RWHUAC, UniProt: P01848*PLUS
#5: Protein T-CELL RECEPTOR BETA CHAIN / TCR HA1.7 BETA CHAIN


Mass: 27943.275 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN / Mutation: C192S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01850

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Protein/peptide / Sugars / Non-polymers , 3 types, 103 molecules C

#3: Protein/peptide HEMAGGLUTININ HA1 PEPTIDE CHAIN


Mass: 1506.807 Da / Num. of mol.: 1 / Fragment: ANTIGEN PEPTIDE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) H3N2 subtype (virus) / Genus: Influenzavirus A / Species: Influenza A virus / Production host: Escherichia coli (E. coli) / References: UniProt: P03437
#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 / 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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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: 3.17 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 11% PEG 8000, 1 M NaCl, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Crystal grow
*PLUS
Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
211 %PEG80001reservoir
31 M1reservoirNaCl
4100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 37312 / Num. obs: 37159 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 59.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.221 / Num. unique all: 3680 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 25 Å
Reflection shell
*PLUS
% possible obs: 99.8 % / Mean I/σ(I) obs: 7.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementResolution: 2.6→19.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1407758.26 / 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
Rfree0.255 1871 5 %RANDOM
Rwork0.221 ---
all-37122 --
obs-37122 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.68 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å23.42 Å2
2--6.74 Å20 Å2
3----6.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-20 Å
Luzzati sigma a0.38 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 28 100 6644
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.692
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.952.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.377 184 5 %
Rwork0.328 3488 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.377 / % reflection Rfree: 5 % / Rfactor Rwork: 0.328

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