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Basic information

Entry
Database: PDB / ID: 5til
TitleMurine class I major histocompatibility complex H-2 Db in complex with LCMV-derived GP33 altered peptide V3P and T-cell receptor P14
Components
  • Alpha chain of murine P14 T cell receptor
  • Beta chain of murine T cell receptor P14
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Pre-glycoprotein polyprotein GP complex
  • alpha chain of P14 T cell receptor
KeywordsIMMUNE SYSTEM / LCMV / MHC class I / T cell receptor
Function / homology
Function and homology information


TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / host cell Golgi membrane / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / 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 / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / H-2 class I histocompatibility antigen, D-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.83 Å
AuthorsAchour, A. / Sandalova, T. / Allerbring, E.B.
CitationJournal: To be published
Title: Ternary complexes of TCR P14 give insights into the mechanisms behind reestablishment of CTL responses against a viral escape mutant
Authors: Allerbring, E. / Duru, A.D. / Sun, R. / Han, X. / Uchtenhagen, H. / Madhurantakam, C. / Popov, A. / Markoba, N. / Talyzina, A. / Nygren, P.A. / Sandalova, T. / Achour, A.
History
DepositionOct 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Pre-glycoprotein polyprotein GP complex
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Pre-glycoprotein polyprotein GP complex
G: alpha chain of P14 T cell receptor
H: Beta chain of murine T cell receptor P14
K: Alpha chain of murine P14 T cell receptor
L: Beta chain of murine T cell receptor P14


Theoretical massNumber of molelcules
Total (without water)184,12910
Polymers184,12910
Non-polymers00
Water72140
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Pre-glycoprotein polyprotein GP complex
G: alpha chain of P14 T cell receptor
H: Beta chain of murine T cell receptor P14


Theoretical massNumber of molelcules
Total (without water)94,5565
Polymers94,5565
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Pre-glycoprotein polyprotein GP complex
K: Alpha chain of murine P14 T cell receptor
L: Beta chain of murine T cell receptor P14


Theoretical massNumber of molelcules
Total (without water)89,5735
Polymers89,5735
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.224, 66.698, 523.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D
13B
23E
14G
24K
15H
25L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A3 - 175
2112D3 - 175
1122A176 - 276
2122D176 - 276
1132B1 - 99
2132E1 - 99
1145G8 - 120
2145K8 - 120
1155H13 - 130
2155L13 - 130

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.065579, -0.978502, -0.195535), (-0.977334, -0.102514, 0.185225), (-0.201288, 0.178956, -0.963046)-44.37258, -22.15164, -129.46732

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Components

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Protein , 5 types, 8 molecules ADBEGHLK

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32087.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P01887
#4: Protein alpha chain of P14 T cell receptor


Mass: 23072.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#5: Protein Beta chain of murine T cell receptor P14


Mass: 26647.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#6: Protein Alpha chain of murine P14 T cell receptor


Mass: 18090.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Protein/peptide / Non-polymers , 2 types, 42 molecules CF

#3: Protein/peptide Pre-glycoprotein polyprotein GP complex


Mass: 1043.215 Da / Num. of mol.: 2 / Fragment: gp33 peptide, UNP residues 33-41 / Mutation: Val35Pro, Cys41Met / Source method: obtained synthetically
Source: (synth.) Lymphocytic choriomeningitis mammarenavirus
References: UniProt: Q9QDK7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 6000, Tris HCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.83→52.49 Å / Num. obs: 51497 / % possible obs: 97.8 % / Redundancy: 3 % / Biso Wilson estimate: 79.7 Å2 / Rsym value: 0.125 / Net I/σ(I): 6.1
Reflection shellResolution: 2.83→2.98 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.56 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.83→52.49 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.87 / SU B: 16.934 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 1.825 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27526 2615 5.1 %RANDOM
Rwork0.21938 ---
obs0.22224 48845 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.942 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å2-0 Å2
2---0.8 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.83→52.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11811 0 0 40 11851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912154
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211015
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.93216494
X-RAY DIFFRACTIONr_angle_other_deg0.932325389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.13751448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46223.727609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.178151968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7971580
X-RAY DIFFRACTIONr_chiral_restr0.0810.21702
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113793
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022977
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5297.3175834
X-RAY DIFFRACTIONr_mcbond_other4.5217.3175833
X-RAY DIFFRACTIONr_mcangle_it7.23110.967268
X-RAY DIFFRACTIONr_mcangle_other7.23210.9627269
X-RAY DIFFRACTIONr_scbond_it4.3697.7026320
X-RAY DIFFRACTIONr_scbond_other4.3687.76318
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.10411.4079226
X-RAY DIFFRACTIONr_long_range_B_refined10.59657.20512797
X-RAY DIFFRACTIONr_long_range_B_other10.59657.21312798
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1737medium positional0.030.5
2A992medium positional0.020.5
3B994medium positional0.430.5
4G651medium positional0.210.5
5H687medium positional0.330.5
4G1059loose positional0.465
5H1075loose positional0.575
1A1018tight thermal5.870.5
2A591tight thermal6.210.5
3B576tight thermal5.670.5
1A1737medium thermal6.782
2A992medium thermal7.612
3B994medium thermal5.862
4G651medium thermal4.212
5H687medium thermal4.382
4G1059loose thermal5.6210
5H1075loose thermal5.7910
LS refinement shellResolution: 2.83→2.904 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 165 -
Rwork0.339 3039 -
obs--82.85 %

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