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- PDB-1n3n: Crystal structure of a mycobacterial hsp60 epitope with the murin... -

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Basic information

Entry
Database: PDB / ID: 1n3n
TitleCrystal structure of a mycobacterial hsp60 epitope with the murine class I MHC molecule H-2Db
Components
  • BETA-2-MICROGLOBULIN
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
  • mycobacterial hsp60 decameric epitope
KeywordsIMMUNE SYSTEM / Immunoglobulin fold
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 / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum 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 endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / 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 / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
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 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCiatto, C. / Capitani, G. / Tissot, A.C. / Pecorari, F. / Pluckthun, A. / Grutter, M.G.
CitationJournal: FEBS Lett. / Year: 2003
Title: Structural analysis of mycobacterial and murine hsp60 epitopes in complex with the class I MHC molecule H-2D(b)
Authors: Ciatto, C. / Capitani, G. / Tissot, A.C. / Pecorari, F. / Plueckthun, A. / Gruetter, M.G.
History
DepositionOct 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
D: BETA-2-MICROGLOBULIN
E: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
F: BETA-2-MICROGLOBULIN
G: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
H: BETA-2-MICROGLOBULIN
I: mycobacterial hsp60 decameric epitope
J: mycobacterial hsp60 decameric epitope
K: mycobacterial hsp60 decameric epitope
L: mycobacterial hsp60 decameric epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,67014
Polymers180,47812
Non-polymers1922
Water3,405189
1
A: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
I: mycobacterial hsp60 decameric epitope


Theoretical massNumber of molelcules
Total (without water)45,1193
Polymers45,1193
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-18 kcal/mol
Surface area19180 Å2
MethodPISA
2
G: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
H: BETA-2-MICROGLOBULIN
L: mycobacterial hsp60 decameric epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2164
Polymers45,1193
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-32 kcal/mol
Surface area19060 Å2
MethodPISA
3
E: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
F: BETA-2-MICROGLOBULIN
K: mycobacterial hsp60 decameric epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2164
Polymers45,1193
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-33 kcal/mol
Surface area19040 Å2
MethodPISA
4
C: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
D: BETA-2-MICROGLOBULIN
J: mycobacterial hsp60 decameric epitope


Theoretical massNumber of molelcules
Total (without water)45,1193
Polymers45,1193
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-18 kcal/mol
Surface area19110 Å2
MethodPISA
5
G: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
H: BETA-2-MICROGLOBULIN
L: mycobacterial hsp60 decameric epitope
hetero molecules

C: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
D: BETA-2-MICROGLOBULIN
J: mycobacterial hsp60 decameric epitope


Theoretical massNumber of molelcules
Total (without water)90,3357
Polymers90,2396
Non-polymers961
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9500 Å2
ΔGint-58 kcal/mol
Surface area36880 Å2
MethodPISA
6
E: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
F: BETA-2-MICROGLOBULIN
K: mycobacterial hsp60 decameric epitope
hetero molecules

A: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
I: mycobacterial hsp60 decameric epitope


Theoretical massNumber of molelcules
Total (without water)90,3357
Polymers90,2396
Non-polymers961
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9510 Å2
ΔGint-60 kcal/mol
Surface area36920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.276, 122.995, 150.833
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly consists of one alpha chain, one beta-2 microglobulin chain, and a bound peptide antigen

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Components

#1: Protein
H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN


Mass: 32470.111 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein
BETA-2-MICROGLOBULIN


Mass: 11704.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide
mycobacterial hsp60 decameric epitope


Mass: 945.029 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: SOLID-PHASE PEPTIDE SYNTHESIS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.35 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonim sulfate, glycerol, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
2150 mM1dropNaCl
320 mMTris1droppH8.0
42.0 Mammonium sulfate1reservoir
515 %(v/v)glycerol1reservoir
60.1 MTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.872
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 4, 2000
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 47412 / Num. obs: 47412 / % possible obs: 99.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 3→3.11 Å / % possible all: 100
Reflection
*PLUS
Highest resolution: 3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 3.8 % / Num. unique obs: 4725 / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.307 1336 random
Rwork0.246 --
all-44948 -
obs-44948 -
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12604 0 10 189 12803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.54
Refinement
*PLUS
Highest resolution: 3 Å / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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