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- PDB-7lli: Stimulatory immune receptor protein complex -

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Basic information

Entry
Database: PDB / ID: 7lli
TitleStimulatory immune receptor protein complex
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • T cell receptor delta variable 3
  • T cell receptor gamma variable 8
KeywordsIMMUNE SYSTEM / Immune receptor complex / metabolite immunity
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / T cell receptor complex / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / T cell receptor complex / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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 ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-2LJ / T cell receptor gamma variable 8 / T cell receptor delta variable 3 / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRice, M.T. / Littler, D.R. / Rossjohn, J. / Gully, B.S.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)FL160100049 Australia
Australian Research Council (ARC)DP200103462 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Recognition of the antigen-presenting molecule MR1 by a V delta 3 + gamma delta T cell receptor.
Authors: Rice, M.T. / von Borstel, A. / Chevour, P. / Awad, W. / Howson, L.J. / Littler, D.R. / Gherardin, N.A. / Le Nours, J. / Giles, E.M. / Berry, R. / Godfrey, D.I. / Davey, M.S. / Rossjohn, J. / Gully, B.S.
History
DepositionFeb 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
K: T cell receptor gamma variable 8
L: T cell receptor delta variable 3
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
E: T cell receptor gamma variable 8
F: T cell receptor delta variable 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,55010
Polymers190,9178
Non-polymers6332
Water00
1
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
K: T cell receptor gamma variable 8
L: T cell receptor delta variable 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7755
Polymers95,4584
Non-polymers3161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
E: T cell receptor gamma variable 8
F: T cell receptor delta variable 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7755
Polymers95,4584
Non-polymers3161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)296.976, 296.976, 122.635
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_1ens_2chain "B"
d_2ens_2chain "D"
d_1ens_3chain "E"
d_2ens_3chain "K"
d_1ens_4(chain "F" and resid 3 through 212)
d_2ens_4(chain "L" and resid 3 through 212)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METVALF1 - 263
d_12ens_15OU5OUG
d_21ens_1METVALA1 - 263
d_22ens_15OU5OUB
d_11ens_2ILEASPH1 - 98
d_21ens_2ILEASPC1 - 98
d_11ens_3ARGASPI1 - 237
d_21ens_3ARGASPD1 - 237
d_11ens_4ASPPROJ2 - 211
d_21ens_4ASPPROE1 - 210

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

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Components

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31711.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein T cell receptor gamma variable 8


Mass: 27757.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRGV8, TCRGV8, TRGV8 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C4DH27
#4: Protein T cell receptor delta variable 3


Mass: 24109.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRDV3, hDV103S1, TRDV3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0JD37
#5: Chemical ChemComp-2LJ / 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


Mass: 316.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 5.45 Å3/Da / Density % sol: 77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 30-40% PEG 400, 0.1/0.2 HEPES pH 7.5, 0.2M MgCl2 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 3.2→88.75 Å / Num. obs: 66481 / % possible obs: 99.9 % / Redundancy: 8.4 % / Biso Wilson estimate: 73.38 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.9
Reflection shellResolution: 3.2→3.28 Å / Num. unique obs: 4465 / CC1/2: 0.77 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GUP, 1TVD, 4LFH, 5D5M

4gup

1tvd

4lfh

5d5m


Resolution: 3.2→88.75 Å / Cross valid method: FREE R-VALUE / σ(F): 461.7 / Phase error: 29.6049
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2629 2008 3.02 %
Rwork0.2438 64427 -
obs0.2528 66435 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.73 Å2
Refinement stepCycle: LAST / Resolution: 3.2→88.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13157 0 44 0 13201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002113567
X-RAY DIFFRACTIONf_angle_d0.608818442
X-RAY DIFFRACTIONf_chiral_restr0.04321961
X-RAY DIFFRACTIONf_plane_restr0.00382396
X-RAY DIFFRACTIONf_dihedral_angle_d4.56221805
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FX-RAY DIFFRACTIONTorsion NCS0.991114492504
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS0.94458005664
ens_3d_2KX-RAY DIFFRACTIONTorsion NCS1.27165784102
ens_4d_2LX-RAY DIFFRACTIONTorsion NCS0.883595791645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.37071430.34674582X-RAY DIFFRACTION95.52
3.28-3.370.30681440.33424586X-RAY DIFFRACTION96.81
3.37-3.470.32151400.31394585X-RAY DIFFRACTION96.93
3.47-3.580.33681420.30074651X-RAY DIFFRACTION96.98
3.58-3.710.31281480.28484588X-RAY DIFFRACTION96.81
3.71-3.860.30651420.28024590X-RAY DIFFRACTION96.98
3.86-4.030.30441430.27514606X-RAY DIFFRACTION96.97
4.03-4.240.24611400.25024617X-RAY DIFFRACTION97.02
4.24-4.510.24521450.22274625X-RAY DIFFRACTION96.96
4.51-4.860.20421410.21114598X-RAY DIFFRACTION96.92
4.86-5.350.24171450.2124590X-RAY DIFFRACTION96.92
5.35-6.120.24191450.23524609X-RAY DIFFRACTION96.89
6.12-7.710.22891420.23654605X-RAY DIFFRACTION96.99
7.71-88.750.25961460.23664597X-RAY DIFFRACTION96.56
Refinement TLS params.Method: refined / Origin x: 27.658509576 Å / Origin y: 47.7910571246 Å / Origin z: -51.4057284633 Å
111213212223313233
T0.0764215567124 Å2-0.0606533796494 Å2-0.00738533882691 Å2-0.0597269299857 Å2-0.00553104461503 Å2--1.88389136406 Å2
L0.299176969257 °2-0.165753650788 °20.0913779567498 °2-0.111757002396 °2-0.0565206293519 °2--0.265227960123 °2
S0.0914405285812 Å °-0.196054909319 Å °-0.0272080921134 Å °-0.222054431777 Å °-0.0577422374466 Å °0.0304196133829 Å °0.325384319659 Å °-0.236698965273 Å °0.0910538995576 Å °
Refinement TLS groupSelection details: all

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