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- PDB-1zs8: Crystal Structure of the Murine MHC Class Ib Molecule M10.5 -

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Basic information

Entry
Database: PDB / ID: 1zs8
TitleCrystal Structure of the Murine MHC Class Ib Molecule M10.5
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • histocompatibility 2, M region locus 10.5
KeywordsIMMUNE SYSTEM / major histocompatibility complex / MHC / vomeronasal organ / VNO / V2R receptors / pheromone receptors / beta-2-microglobulin / peptides
Function / homology
Function and homology information


antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 endogenous peptide antigen via MHC class Ib / 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 / Major histocompatibility complex class Ib M10.5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsOlson, R. / Huey-Tubman, K.E. / Dulac, C. / Bjorkman, P.J.
CitationJournal: Plos Biol. / Year: 2005
Title: Structure of a pheromone receptor-associated MHC molecule with an open and empty groove.
Authors: Olson, R. / Huey-Tubman, K.E. / Dulac, C. / Bjorkman, P.J.
History
DepositionJul 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: histocompatibility 2, M region locus 10.5
B: Beta-2-microglobulin
C: histocompatibility 2, M region locus 10.5
D: Beta-2-microglobulin
E: histocompatibility 2, M region locus 10.5
F: Beta-2-microglobulin
G: histocompatibility 2, M region locus 10.5
H: Beta-2-microglobulin
I: histocompatibility 2, M region locus 10.5
J: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,95415
Polymers215,84710
Non-polymers1,1065
Water0
1
A: histocompatibility 2, M region locus 10.5
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3913
Polymers43,1692
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-11 kcal/mol
Surface area17360 Å2
MethodPISA
2
C: histocompatibility 2, M region locus 10.5
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3913
Polymers43,1692
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-11 kcal/mol
Surface area17360 Å2
MethodPISA
3
E: histocompatibility 2, M region locus 10.5
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3913
Polymers43,1692
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-11 kcal/mol
Surface area17370 Å2
MethodPISA
4
G: histocompatibility 2, M region locus 10.5
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3913
Polymers43,1692
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-10 kcal/mol
Surface area17370 Å2
MethodPISA
5
I: histocompatibility 2, M region locus 10.5
J: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3913
Polymers43,1692
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-11 kcal/mol
Surface area17370 Å2
MethodPISA
6
G: histocompatibility 2, M region locus 10.5
H: Beta-2-microglobulin
hetero molecules

E: histocompatibility 2, M region locus 10.5
F: Beta-2-microglobulin
hetero molecules

C: histocompatibility 2, M region locus 10.5
D: Beta-2-microglobulin
hetero molecules

A: histocompatibility 2, M region locus 10.5
B: Beta-2-microglobulin
I: histocompatibility 2, M region locus 10.5
J: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,95415
Polymers215,84710
Non-polymers1,1065
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation2_554-x+1/2,-y,z-1/21
crystal symmetry operation3_545-x,y-1/2,-z+1/21
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
identity operation1_555x,y,z1
Buried area16030 Å2
ΔGint-78 kcal/mol
Surface area83210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.110, 134.710, 149.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly consists of chains A and B. To generate the asymmetric unit, the following transformations are required: MTRIX1 1 1.000000 0.000000 0.000000 0.00000 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 MTRIX1 2 0.983930 -0.015240 -0.177890 21.04371 MTRIX2 2 0.157760 -0.392300 0.906210 15.20531 MTRIX3 2 -0.083600 -0.919710 -0.383590 123.20857 MTRIX1 3 -0.995850 0.007030 0.090700 21.34146 MTRIX2 3 0.050020 -0.790450 0.610480 41.21530 MTRIX3 3 0.075980 0.612480 0.786820 -23.46491 MTRIX1 4 -0.990940 -0.026570 0.131680 6.34136 MTRIX2 4 -0.118920 -0.282390 -0.951900 47.17054 MTRIX3 4 0.062480 -0.958930 0.276670 112.45370 MTRIX1 5 0.986590 0.035450 -0.159320 33.74422 MTRIX2 5 -0.062000 -0.821580 -0.566710 38.04500 MTRIX3 5 -0.150980 0.568990 -0.808360 91.82664

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Components

#1: Protein
histocompatibility 2, M region locus 10.5 /


Mass: 31421.334 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: M10.5 / Plasmid: pACUW31 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tn5 / References: GenBank: 29244030, UniProt: Q860W6*PLUS
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pACUW31 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tn5 / References: UniProt: P61769
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M imidazole, 20% PEG 1000, 0.2 M calcium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 12.3.111.11587
SYNCHROTRONSSRL BL9-221.00879
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDApr 3, 2005double crystal monochromator
ADSC QUANTUM 3152CCDApr 27, 2005double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
21.008791
ReflectionResolution: 3→99 Å / Num. all: 46977 / Num. obs: 46977 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 76.6 Å2 / Rmerge(I) obs: 0.156 / Rsym value: 0.156 / Χ2: 1.106 / Net I/σ(I): 9
Reflection shellResolution: 3→3.11 Å / % possible obs: 64.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 2.7 / Num. measured obs: 3287 / Num. unique all: 3287 / Rsym value: 0.535 / Χ2: 0.814 / % possible all: 64.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
PDB_EXTRACT1.601data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K8D (confirmed with 3FRU)

1k8d

3fru


Resolution: 3→56.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2322336.75 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.308 2355 5 %Thin shell method
Rwork0.307 ---
all0.307 46898 --
obs0.307 46898 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 98.338 Å2 / ksol: 0.424 e/Å3
Displacement parametersBiso mean: 59.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---3.09 Å20 Å2
3---2.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.55 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3→56.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13665 0 70 0 13735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.83
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.463 314 4.8 %
Rwork0.438 6168 -
obs-6320 77.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2carbohydrate.param

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