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- PDB-7llj: Inhibitory immune receptor protein complex -

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Basic information

Entry
Database: PDB / ID: 7llj
TitleInhibitory 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 / antigen processing and presentation of peptide antigen via MHC class I / 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 / antigen processing and presentation of peptide antigen via MHC class I / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma 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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-30W / 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: 3.15 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
K: T cell receptor gamma variable 8
L: T cell receptor delta variable 3
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
A: T cell receptor gamma variable 8
B: T cell receptor delta variable 3
E: Major histocompatibility complex class I-related gene protein
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,38310
Polymers190,9178
Non-polymers4662
Water00
1
K: T cell receptor gamma variable 8
L: T cell receptor delta variable 3
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6925
Polymers95,4584
Non-polymers2331
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: T cell receptor gamma variable 8
B: T cell receptor delta variable 3
E: Major histocompatibility complex class I-related gene protein
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6925
Polymers95,4584
Non-polymers2331
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)297.549, 297.549, 120.371
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_1(chain "A" and resid 14 through 249)
d_2ens_1chain "K"
d_1ens_2(chain "B" and (resid 2 through 138 or resid 140 through 213))
d_2ens_2chain "L"
d_1ens_3chain "C"
d_2ens_3(chain "E" and (resid 0 through 244 or resid 249 through 269 or resid 301))
d_1ens_4chain "D"
d_2ens_4chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGALAF1 - 236
d_21ens_1ARGALAA1 - 236
d_11ens_2SERSERG1 - 137
d_12ens_2ASPGLUG139 - 212
d_21ens_2SERGLUB1 - 211
d_11ens_3METVALC1 - 263
d_12ens_3AFPAFPD
d_21ens_3METILEH1 - 242
d_22ens_3GLNVALH245 - 265
d_23ens_3AFPAFPI
d_11ens_4ILEASPE1 - 97
d_21ens_4ILEASPJ1 - 97

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

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Components

#1: 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 / Production host: Escherichia coli (E. coli)
#2: 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 / Production host: Escherichia coli (E. coli)
#3: 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
#4: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
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
#5: Chemical ChemComp-30W / N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide / Acetyl 6-formylpterin


Mass: 233.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7N5O3 / 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: 5.37 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: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.15→85.89 Å / Num. obs: 68693 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 75.03 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.6
Reflection shellResolution: 3.15→3.22 Å / Num. unique obs: 4609 / CC1/2: 0.713

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Coot1.17.1_3660model building
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GUP, 1TVD, 4LFH, 5D5M

4gup

1tvd

4lfh

5d5m


Resolution: 3.15→75.71 Å / Cross valid method: FREE R-VALUE / σ(F): 606.25 / Phase error: 32.1747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2761 1993 2.9 %
Rwork0.2405 66669 -
obs0.248 68662 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 100.16 Å2
Refinement stepCycle: LAST / Resolution: 3.15→75.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13158 0 32 0 13190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001913556
X-RAY DIFFRACTIONf_angle_d0.53218425
X-RAY DIFFRACTIONf_chiral_restr0.04231954
X-RAY DIFFRACTIONf_plane_restr0.00362405
X-RAY DIFFRACTIONf_dihedral_angle_d4.26391799
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FX-RAY DIFFRACTIONTorsion NCS1.18205748951
ens_2d_2LX-RAY DIFFRACTIONTorsion NCS0.979424579834
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS1.15210590621
ens_4d_2EX-RAY DIFFRACTIONTorsion NCS0.765014239678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.230.34451410.33124721X-RAY DIFFRACTION96.96
3.23-3.320.35171430.32314758X-RAY DIFFRACTION97.04
3.32-3.410.31161410.30674785X-RAY DIFFRACTION97.12
3.41-3.520.33021450.29054797X-RAY DIFFRACTION97.01
3.52-3.650.29271450.28464754X-RAY DIFFRACTION97.04
3.65-3.80.31141400.26734737X-RAY DIFFRACTION97.07
3.8-3.970.27381420.26384754X-RAY DIFFRACTION97.08
3.97-4.180.2691430.25444758X-RAY DIFFRACTION97.08
4.18-4.440.30161420.22624789X-RAY DIFFRACTION97.1
4.44-4.780.29121410.2174768X-RAY DIFFRACTION97.11
4.78-5.260.2331420.21434755X-RAY DIFFRACTION96.96
5.26-6.020.27231460.23284759X-RAY DIFFRACTION97
6.02-7.590.26231360.23584775X-RAY DIFFRACTION97.23
7.59-75.710.25531460.22664759X-RAY DIFFRACTION96.89
Refinement TLS params.Method: refined / Origin x: 27.7200058654 Å / Origin y: 47.8568329463 Å / Origin z: 47.0513047283 Å
111213212223313233
T0.330608079628 Å2-0.0717215883681 Å2-0.0215811891336 Å2-0.282825418767 Å20.0131253503777 Å2--1.66983486264 Å2
L0.0897415256084 °2-0.0599170366147 °20.0832774302688 °2-0.0340949176355 °2-0.0389726879819 °2--0.244244417739 °2
S0.0770101172165 Å °-0.0974853895269 Å °-0.0164632304184 Å °-0.0959541520085 Å °-0.0439901054456 Å °0.00510481711933 Å °0.234076605982 Å °-0.15154855101 Å °0.022452800047 Å °
Refinement TLS groupSelection details: all

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