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- PDB-1c16: CRYSTAL STRUCTURE ANALYSIS OF THE GAMMA/DELTA T CELL LIGAND T22 -

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Basic information

Entry
Database: PDB / ID: 1c16
TitleCRYSTAL STRUCTURE ANALYSIS OF THE GAMMA/DELTA T CELL LIGAND T22
Components
  • MHC-LIKE PROTEIN T22
  • PROTEIN (BETA-2-MICROGLOBULIN)
KeywordsIMMUNE SYSTEM / NON-CLASSICAL MHC-LIKE / MAJOR HISTOCOMPATIBILITY / BETA2-MICROGLOBULIN
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Neutrophil degranulation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Neutrophil degranulation / 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 / 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 / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / 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 / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / Histocompatibility 2, T region locus 22
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsWingren, C. / Crowley, M.P. / Degano, M. / Chien, Y. / Wilson, I.A.
CitationJournal: Science / Year: 2000
Title: Crystal structure of a gammadelta T cell receptor ligand T22: a truncated MHC-like fold.
Authors: Wingren, C. / Crowley, M.P. / Degano, M. / Chien, Y. / Wilson, I.A.
History
DepositionJul 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC-LIKE PROTEIN T22
B: PROTEIN (BETA-2-MICROGLOBULIN)
C: MHC-LIKE PROTEIN T22
D: PROTEIN (BETA-2-MICROGLOBULIN)
E: MHC-LIKE PROTEIN T22
F: PROTEIN (BETA-2-MICROGLOBULIN)
G: MHC-LIKE PROTEIN T22
H: PROTEIN (BETA-2-MICROGLOBULIN)


Theoretical massNumber of molelcules
Total (without water)166,6718
Polymers166,6718
Non-polymers00
Water0
1
A: MHC-LIKE PROTEIN T22
B: PROTEIN (BETA-2-MICROGLOBULIN)


Theoretical massNumber of molelcules
Total (without water)41,6682
Polymers41,6682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-9 kcal/mol
Surface area20050 Å2
MethodPISA
2
C: MHC-LIKE PROTEIN T22
D: PROTEIN (BETA-2-MICROGLOBULIN)


Theoretical massNumber of molelcules
Total (without water)41,6682
Polymers41,6682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-9 kcal/mol
Surface area19580 Å2
MethodPISA
3
E: MHC-LIKE PROTEIN T22
F: PROTEIN (BETA-2-MICROGLOBULIN)


Theoretical massNumber of molelcules
Total (without water)41,6682
Polymers41,6682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-9 kcal/mol
Surface area19400 Å2
MethodPISA
4
G: MHC-LIKE PROTEIN T22
H: PROTEIN (BETA-2-MICROGLOBULIN)


Theoretical massNumber of molelcules
Total (without water)41,6682
Polymers41,6682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-9 kcal/mol
Surface area19880 Å2
MethodPISA
5
A: MHC-LIKE PROTEIN T22
B: PROTEIN (BETA-2-MICROGLOBULIN)
C: MHC-LIKE PROTEIN T22
D: PROTEIN (BETA-2-MICROGLOBULIN)

E: MHC-LIKE PROTEIN T22
F: PROTEIN (BETA-2-MICROGLOBULIN)
G: MHC-LIKE PROTEIN T22
H: PROTEIN (BETA-2-MICROGLOBULIN)


Theoretical massNumber of molelcules
Total (without water)166,6718
Polymers166,6718
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456x-1/2,-y+1/2,-z+11
Buried area16220 Å2
ΔGint-69 kcal/mol
Surface area72040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.110, 91.470, 122.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
MHC-LIKE PROTEIN T22


Mass: 29919.523 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q31615
#2: Protein
PROTEIN (BETA-2-MICROGLOBULIN)


Mass: 11748.160 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61769

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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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal grow
*PLUS
pH: 5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein11
20.1 Mimidazole-maleate11
30.2 Mcalcium acetate11
410 %PEG800011

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 38389 / Num. obs: 34819 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.9 % / Biso Wilson estimate: 62.3 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.6
Reflection shellResolution: 3→50 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.346 / % possible all: 69.2
Reflection shell
*PLUS
Lowest resolution: 3.1 Å / % possible obs: 69.2 % / Num. unique obs: 2597 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementResolution: 3.1→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 260335.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.334 1169 3.4 %RANDOM
Rwork0.284 ---
all0.284 34029 --
obs0.284 29371 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.56 Å2 / ksol: 0.233 e/Å3
Displacement parametersBiso mean: 55.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.9 Å20 Å20 Å2
2---14.05 Å20 Å2
3---9.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.56 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.84 Å
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11652 0 0 0 11652
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d1.01
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.602 177 3.3 %
Rwork0.534 5235 -
obs--95.4 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PA / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Num. reflection Rfree: 1040 / % reflection Rfree: 3 % / Rfactor obs: 0.245 / Rfactor Rfree: 0.301
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.602 / % reflection Rfree: 3.3 % / Rfactor Rwork: 0.534

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