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- PDB-9o4x: Gamma delta T cell receptor bound to CD1d -

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Basic information

Entry
Database: PDB / ID: 9o4x
TitleGamma delta T cell receptor bound to CD1d
Components
  • (T cell receptor ...) x 2
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
KeywordsIMMUNE SYSTEM / T cell receptor complex / gamma delta TCR / Immune complex
Function / homology
Function and homology information


lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding ...lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding / detection of bacterium / cell adhesion molecule binding / positive regulation of T cell proliferation / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / peptide antigen binding / positive regulation of T cell activation / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / basolateral plasma membrane / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / lysosome / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / innate immune response / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
MHC-I family domain / 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 ...MHC-I family domain / 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
sphingomyelin / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsRice, M.T. / Gully, B.S. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: gamma delta T cell receptor bound to CD1d
Authors: Rice, M.T. / Gully, B.S. / Rossjohn, J.
History
DepositionApr 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-2-microglobulin
D: T cell receptor delta chain
G: T cell receptor gamma chain
A: Antigen-presenting glycoprotein CD1d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9809
Polymers90,8574
Non-polymers2,1235
Water00
1
B: Beta-2-microglobulin
A: Antigen-presenting glycoprotein CD1d
hetero molecules

D: T cell receptor delta chain
G: T cell receptor gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9809
Polymers90,8574
Non-polymers2,1235
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
Buried area10400 Å2
ΔGint-28 kcal/mol
Surface area38770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.093, 178.093, 75.428
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 2 types, 2 molecules BA

#1: Protein 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 / Production host: Homo sapiens (human) / References: UniProt: P61769
#4: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 31074.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Production host: Homo sapiens (human) / References: UniProt: P15813

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T cell receptor ... , 2 types, 2 molecules DG

#2: Protein T cell receptor delta chain


Mass: 22211.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein T cell receptor gamma chain


Mass: 25823.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 3 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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

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Non-polymers , 2 types, 2 molecules

#7: Chemical ChemComp-FO4 / sphingomyelin


Mass: 814.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H94N2O6P / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM

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Details

Has ligand of interestY
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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 3350, 0.05M CBTP pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97958 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.86→46.65 Å / Num. obs: 28516 / % possible obs: 99.8 % / Redundancy: 10.4 % / Biso Wilson estimate: 68.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.4
Reflection shellResolution: 2.86→3.02 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4072 / CC1/2: 0.75 / Rpim(I) all: 0.491 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→46.65 Å / SU ML: 0.3855 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1399
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2553 1999 7.02 %
Rwork0.2149 26464 -
obs0.2177 28463 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.59 Å2
Refinement stepCycle: LAST / Resolution: 2.86→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6386 0 142 0 6528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00466713
X-RAY DIFFRACTIONf_angle_d0.94259100
X-RAY DIFFRACTIONf_chiral_restr0.0554994
X-RAY DIFFRACTIONf_plane_restr0.00631139
X-RAY DIFFRACTIONf_dihedral_angle_d17.34142566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.930.38881370.33081821X-RAY DIFFRACTION97.17
2.94-3.010.34421410.31171862X-RAY DIFFRACTION100
3.01-3.10.35061400.29771845X-RAY DIFFRACTION100
3.1-3.20.36971410.30761863X-RAY DIFFRACTION100
3.2-3.320.35371410.27761861X-RAY DIFFRACTION100
3.32-3.450.28481410.25281875X-RAY DIFFRACTION100
3.45-3.610.26941420.24821878X-RAY DIFFRACTION100
3.61-3.80.28871410.23011871X-RAY DIFFRACTION99.95
3.8-4.040.26241420.22361879X-RAY DIFFRACTION100
4.04-4.350.21191420.1831888X-RAY DIFFRACTION100
4.35-4.780.19121450.16351902X-RAY DIFFRACTION100
4.78-5.470.2411450.18011922X-RAY DIFFRACTION100
5.48-6.890.25241470.20371945X-RAY DIFFRACTION100
6.89-46.650.21341540.18962052X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 58.961 Å / Origin y: -26.295 Å / Origin z: 14.05 Å
111213212223313233
T0.387904126113 Å2-0.0762846173692 Å2-0.0478246028086 Å2-0.412966421114 Å2-0.0139230043134 Å2--0.474989099933 Å2
L1.73546771918 °2-1.02291998397 °2-1.03079799995 °2-1.1225591592 °20.697529274695 °2--1.31252455888 °2
S0.143095898843 Å °0.210745285267 Å °0.251300980422 Å °-0.0730357448054 Å °-0.0545095433523 Å °-0.211197024489 Å °-0.261759442719 Å °-0.00641932230203 Å °-0.094450698086 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:99 ) OR ( CHAIN D AND ( RESID 5:201 OR RESID 301:301 ) ) OR ( CHAIN G AND RESID 4:227 ) OR ( CHAIN A AND ( RESID 6:279 OR RESID 301:302 ) )B1 - 99
2X-RAY DIFFRACTION1( CHAIN B AND RESID 1:99 ) OR ( CHAIN D AND ( RESID 5:201 OR RESID 301:301 ) ) OR ( CHAIN G AND RESID 4:227 ) OR ( CHAIN A AND ( RESID 6:279 OR RESID 301:302 ) )D5 - 201
3X-RAY DIFFRACTION1( CHAIN B AND RESID 1:99 ) OR ( CHAIN D AND ( RESID 5:201 OR RESID 301:301 ) ) OR ( CHAIN G AND RESID 4:227 ) OR ( CHAIN A AND ( RESID 6:279 OR RESID 301:302 ) )D301
4X-RAY DIFFRACTION1( CHAIN B AND RESID 1:99 ) OR ( CHAIN D AND ( RESID 5:201 OR RESID 301:301 ) ) OR ( CHAIN G AND RESID 4:227 ) OR ( CHAIN A AND ( RESID 6:279 OR RESID 301:302 ) )G4 - 227
5X-RAY DIFFRACTION1( CHAIN B AND RESID 1:99 ) OR ( CHAIN D AND ( RESID 5:201 OR RESID 301:301 ) ) OR ( CHAIN G AND RESID 4:227 ) OR ( CHAIN A AND ( RESID 6:279 OR RESID 301:302 ) )A6 - 279
6X-RAY DIFFRACTION1( CHAIN B AND RESID 1:99 ) OR ( CHAIN D AND ( RESID 5:201 OR RESID 301:301 ) ) OR ( CHAIN G AND RESID 4:227 ) OR ( CHAIN A AND ( RESID 6:279 OR RESID 301:302 ) )A301 - 302

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