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- PDB-5til: Murine class I major histocompatibility complex H-2 Db in complex... -

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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-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


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 I via ER pathway, TAP-dependent / host cell Golgi membrane / cellular defense response / receptor-mediated endocytosis of virus by host cell ...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 I via ER pathway, TAP-dependent / host cell Golgi membrane / cellular defense response / receptor-mediated endocytosis of virus by host cell / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / MHC class I protein complex / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / host cell endoplasmic reticulum membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / metal ion binding / membrane / plasma membrane / cytosol
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 / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


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


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

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Details

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: 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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