[English] 日本語
Yorodumi
- PDB-4ww2: Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Cha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ww2
TitleCrystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8, Antigen-presenting glycoprotein CD1d, and Beta-2-microglobulin
Components
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulinBeta-2 microglobulin
  • TCR Alpha Chain-TRAV21-TRAJ8
  • TCR Beta Chain-TRBV7-8
KeywordsIMMUNE SYSTEM / Natural Killer T Cells / Immunity
Function / homology
Function and homology information


lipid antigen binding / T cell selection / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / alpha-beta T cell receptor complex / positive regulation of innate immune response / heterotypic cell-cell adhesion ...lipid antigen binding / T cell selection / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / alpha-beta T cell receptor complex / positive regulation of innate immune response / heterotypic cell-cell adhesion / T cell receptor complex / alpha-beta T cell activation / beta-2-microglobulin binding / positive regulation of T cell proliferation / detection of bacterium / cell adhesion molecule binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / histone binding / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / basolateral plasma membrane / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / lysosome / learning or memory / endosome membrane / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome
Similarity search - Function
MHC-I family domain / Domain of unknown function (DUF1968) / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein ...MHC-I family domain / Domain of unknown function (DUF1968) / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / 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 / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-JLS / T cell receptor alpha variable 21 / T cell receptor beta constant 2 / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsLe Nours, J. / Praveena, T. / Pellicci, D. / Gherardin, N.A. / Lim, R.T. / Besra, G. / Keshipeddy, S. / Richardson, S.K. / Howell, A.R. / Gras, S. ...Le Nours, J. / Praveena, T. / Pellicci, D. / Gherardin, N.A. / Lim, R.T. / Besra, G. / Keshipeddy, S. / Richardson, S.K. / Howell, A.R. / Gras, S. / Godfrey, D.I. / Rossjohn, J. / Uldrich, A.P.
CitationJournal: Nat Commun / Year: 2016
Title: Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens.
Authors: Le Nours, J. / Praveena, T. / Pellicci, D.G. / Gherardin, N.A. / Ross, F.J. / Lim, R.T. / Besra, G.S. / Keshipeddy, S. / Richardson, S.K. / Howell, A.R. / Gras, S. / Godfrey, D.I. / Rossjohn, J. / Uldrich, A.P.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TCR Alpha Chain-TRAV21-TRAJ8
B: TCR Beta Chain-TRBV7-8
C: Antigen-presenting glycoprotein CD1d
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2867
Polymers94,0154
Non-polymers1,2713
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.990, 46.300, 124.650
Angle α, β, γ (deg.)90.00, 122.28, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 4 types, 4 molecules ABCF

#1: Protein TCR Alpha Chain-TRAV21-TRAJ8


Mass: 22573.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J279*PLUS
#2: Protein TCR Beta Chain-TRBV7-8


Mass: 27368.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B9*PLUS
#3: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 32324.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Plasmid: pFastBac Dual / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15813
#4: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pFastBac Dual / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769

-
Sugars , 1 types, 2 molecules

#5: 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: 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

-
Non-polymers , 2 types, 171 molecules

#6: Chemical ChemComp-JLS / (15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide / PBS-44


Mass: 828.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H93NO9
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 9-10% PEG 6K 0.1M MES 6.0 4% Ethylene Glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.7108 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7108 Å / Relative weight: 1
ReflectionResolution: 2.48→44.8 Å / Num. obs: 36324 / % possible obs: 99.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 51.78 Å2 / Net I/σ(I): 8.2
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.6 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PO6, 4WW1

2po6

4ww1


Resolution: 2.48→44.8 Å / Cor.coef. Fo:Fc: 0.9347 / Cor.coef. Fo:Fc free: 0.8972 / SU R Cruickshank DPI: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.382 / SU Rfree Blow DPI: 0.252 / SU Rfree Cruickshank DPI: 0.257
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 1815 5 %RANDOM
Rwork0.1957 ---
obs0.1981 36324 99.26 %-
Displacement parametersBiso mean: 56.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.789 Å20 Å2-0.2764 Å2
2---1.6818 Å20 Å2
3---0.8929 Å2
Refine analyzeLuzzati coordinate error obs: 0.394 Å
Refinement stepCycle: LAST / Resolution: 2.48→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6284 0 86 170 6540
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086550HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.038938HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2935SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes967HARMONIC5
X-RAY DIFFRACTIONt_it6550HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion2.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion856SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7043SEMIHARMONIC4
LS refinement shellResolution: 2.48→2.55 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2957 178 6.32 %
Rwork0.247 2640 -
all0.2502 2818 -
obs--99.26 %
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)
13.7317-1.0246-0.88930.39330.36623.40430.03610.40050.1274-0.1331-0.12570.1467-0.0869-0.19630.0896-0.0058-0.12-0.0195-0.23320.0275-0.047234.4937-12.4426-21.8917
22.8926-0.65140.0930.38150.64861.2869-0.0066-0.1155-0.0482-0.01390.01420.1315-0.06170.1153-0.0076-0.0627-0.0002-0.0273-0.24450.0073-0.066845.108-23.2759-10.1966
32.350.3331-1.65090.5059-0.0861.02430.1244-0.7251-0.03540.14890.0011-0.09520.02630.4356-0.1254-0.19950.064-0.0030.3327-0.1033-0.25293.2486-8.416328.3926
4-0.15520.5759-1.19663.7144-2.18095.31320.2735-0.4411-0.71650.46860.2382-0.30480.5380.2459-0.5116-0.40080.0763-0.19290.56870.2278-0.3023.1366-17.701645.2713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ F|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more