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- PDB-1mhc: MODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED ... -

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Basic information

Entry
Database: PDB / ID: 1mhc
TitleMODEL OF MHC CLASS I H2-M3 WITH NONAPEPTIDE FROM RAT ND1 REFINED AT 2.3 ANGSTROMS RESOLUTION
Components
  • (MHC CLASS I ANTIGEN H2-M3) x 2
  • NONAPEPTIDE FROM RAT NADH DEHYDROGENASEPeptide
KeywordsHISTOCOMPATIBILITY ANTIGEN/PEPTIDE / HISTOCOMPATIBILITY ANTIGEN-PEPTIDE complex
Function / homology
Function and homology information


Complex I biogenesis / alpha-beta T cell activation involved in immune response / Respiratory electron transport / response to xenobiotic stimulus => GO:0009410 / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / cis-Golgi network membrane / response to hydroperoxide / Endosomal/Vacuolar pathway / DAP12 interactions ...Complex I biogenesis / alpha-beta T cell activation involved in immune response / Respiratory electron transport / response to xenobiotic stimulus => GO:0009410 / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / cis-Golgi network membrane / response to hydroperoxide / 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 / NADH:ubiquinone reductase (H+-translocating) / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / mitochondrial respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / CD8 receptor binding / cellular defense response / aerobic respiration / 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 / nitric oxide biosynthetic process / Neutrophil degranulation / mitochondrial membrane / 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 / response to organic cyclic compound / 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 / positive regulation of nitric oxide biosynthetic process / 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 / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / membrane => GO:0016020 / learning or memory / early endosome / defense response to Gram-positive bacterium / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / dendrite / neuronal cell body / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / identical protein binding / plasma membrane / cytosol
Similarity search - Function
NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / 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 ...NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / 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 / NADH-ubiquinone oxidoreductase chain 1 / Histocompatibility 2, M region locus 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsWang, C.-R. / Fischer Lindahl, K. / Deisenhofer, J.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3
Authors: Wang, C.R. / Castano, A.R. / Peterson, P.A. / Slaughter, C. / Lindahl, K.F. / Deisenhofer, J.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1991
Title: H-2M3 Encodes the Mhc Class I Molecule Presenting the Maternally Transmitted Antigen of the Mouse
Authors: Wang, C.-R. / Loveland, B.E. / Fischer Lindahl, K.
History
DepositionAug 23, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC CLASS I ANTIGEN H2-M3
B: MHC CLASS I ANTIGEN H2-M3
C: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
D: MHC CLASS I ANTIGEN H2-M3
E: MHC CLASS I ANTIGEN H2-M3
F: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2427
Polymers91,0216
Non-polymers2211
Water6,702372
1
A: MHC CLASS I ANTIGEN H2-M3
B: MHC CLASS I ANTIGEN H2-M3
C: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)45,5103
Polymers45,5103
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-27 kcal/mol
Surface area19540 Å2
MethodPISA
2
D: MHC CLASS I ANTIGEN H2-M3
E: MHC CLASS I ANTIGEN H2-M3
F: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7324
Polymers45,5103
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-24 kcal/mol
Surface area19420 Å2
MethodPISA
3
D: MHC CLASS I ANTIGEN H2-M3
E: MHC CLASS I ANTIGEN H2-M3
F: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE
hetero molecules

A: MHC CLASS I ANTIGEN H2-M3
B: MHC CLASS I ANTIGEN H2-M3
C: NONAPEPTIDE FROM RAT NADH DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)91,2427
Polymers91,0216
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_444x-1,y-1,z-11
Buried area10450 Å2
ΔGint-49 kcal/mol
Surface area37370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.250, 66.100, 55.170
Angle α, β, γ (deg.)102.71, 96.28, 110.19
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO A 210 / 2: CIS PROLINE - PRO B 32 / 3: CIS PROLINE - PRO D 210 / 4: CIS PROLINE - PRO E 32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9585, -0.1906, 0.2119), (-0.2302, -0.9561, 0.1812), (0.1681, -0.2225, -0.9603)4.9129, 38.8128, 28.6944
2given(0.9641, -0.1867, 0.1886), (-0.2217, -0.9573, 0.1854), (0.1459, -0.2206, -0.9644)4.8695, 38.7328, 28.6928
3given(0.9646, -0.1991, 0.1729), (-0.2317, -0.953, 0.1953), (0.1259, -0.2284, -0.9654)4.9692, 38.6988, 28.6453
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 D 2 .. D 182 A 2 .. A 182 0.288 M2 D 183 .. D 275 A 183 .. A 275 0.292 M3 E 1 .. E 99 B 1 .. B 99 0.312

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Components

#1: Protein MHC CLASS I ANTIGEN H2-M3 / MAJOR HISTOCOMPATIBILITY COMPLEX


Mass: 32650.650 Da / Num. of mol.: 2 / Mutation: INS(275(A)-282(A)), INS(275(D)-282(D))
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-M3 B2M / Gene (production host): H2-M3 B2M / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q31093
#2: Protein MHC CLASS I ANTIGEN H2-M3 / MAJOR HISTOCOMPATIBILITY COMPLEX


Mass: 11704.359 Da / Num. of mol.: 2 / Mutation: INS(275(A)-282(A)), INS(275(D)-282(D))
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-M3 B2M / Gene (production host): H2-M3 B2M / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887
#3: Protein/peptide NONAPEPTIDE FROM RAT NADH DEHYDROGENASE / Peptide / ND1


Mass: 1155.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P03889
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 26 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
220 mMTris-HCl1drop
316-18 %PEG80001reservoir
4100 mMHEPES1reservoir
52 %MPD1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 33706 / % possible obs: 70 % / Rmerge(I) obs: 0.079
Reflection
*PLUS
Rmerge(I) obs: 0.079
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.17 Å / % possible obs: 43 %

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.19 --
obs0.19 33706 70 %
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 14 372 6668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.88
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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