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- PDB-1s7t: Crystal structures of the murine class I major histocompatibility... -

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Basic information

Entry
Database: PDB / ID: 1s7t
TitleCrystal structures of the murine class I major histocompatibility complex H-2Kb in complex with LCMV-derived gp33 index peptide and three of its escape variants
Components
  • Beta-2-microglobulin
  • Glycoprotein 9-residue peptide
  • H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / LCMV / MHC class I / immune escape
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 exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / host cell Golgi membrane ...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 exogenous peptide antigen via MHC class I / inner ear development / 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 / peptide antigen binding / 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 / defense response to bacterium / 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 / 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, K-B alpha chain / Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVelloso, L.M. / Michaelsson, J. / Ljunggren, H.G. / Schneider, G. / Achour, A.
CitationJournal: J.Immunol. / Year: 2004
Title: Determination of structural principles underlying three different modes of lymphocytic choriomeningitis virus escape from CTL recognition.
Authors: Velloso, L.M. / Michaelsson, J. / Ljunggren, H.G. / Schneider, G. / Achour, A.
History
DepositionJan 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE CYSTEINE IN THE ORIGINAL SEQUENCE IS REPLACED INTENTIONALLY BY A METHIONINE TO AVOID ...SEQUENCE THE CYSTEINE IN THE ORIGINAL SEQUENCE IS REPLACED INTENTIONALLY BY A METHIONINE TO AVOID OXIDATION OF THE PEPTIDE.

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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, K-B alpha chain
B: Beta-2-microglobulin
C: Glycoprotein 9-residue peptide
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)103,8676
Polymers103,8676
Non-polymers00
Water6,539363
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)51,9343
Polymers51,9343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-27 kcal/mol
Surface area19070 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: Glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)51,9343
Polymers51,9343
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-26 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.298, 92.688, 128.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2KB


Mass: 39200.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K / Plasmid: PET-3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P01901
#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 / Plasmid: PET-3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: P01887
#3: Protein/peptide Glycoprotein 9-residue peptide


Mass: 1029.232 Da / Num. of mol.: 2 / Mutation: Y4F / Source method: obtained synthetically
Details: The peptide was chemically synthesized, the sequence of the peptide is naturally found in Lymphocytic choriomeningitis virus
References: UniProt: P07399
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium/potassium phosphate, Methyl pentane diol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.007 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 47923 / Num. obs: 47348 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 2.29→2.42 Å / % possible all: 92.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N59

1n59


Resolution: 2.3→19.88 Å / SU B: 6.306 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25193 1915 4.1 %RANDOM
Rwork0.20467 ---
obs0.20652 45308 99.21 %-
all-47923 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 27.089 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6258 0 0 363 6621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216442
X-RAY DIFFRACTIONr_bond_other_d0.0020.025566
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.9348750
X-RAY DIFFRACTIONr_angle_other_deg0.805312982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4595760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027166
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021364
X-RAY DIFFRACTIONr_nbd_refined0.1890.21102
X-RAY DIFFRACTIONr_nbd_other0.2360.26313
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.23835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2325
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1520.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5471.53820
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0726176
X-RAY DIFFRACTIONr_scbond_it1.52532622
X-RAY DIFFRACTIONr_scangle_it2.6524.52574
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.297→2.356 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 136
Rwork0.247 2951

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