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- PDB-1mwa: 2C/H-2KBM3/DEV8 ALLOGENEIC COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1mwa
Title2C/H-2KBM3/DEV8 ALLOGENEIC COMPLEX
Components
  • (2C T CELL RECEPTOR ...) x 2
  • DEV8
  • H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
  • MICROGLOBULIN MHC LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Ig domain / antigen recognition / complementarity determining region
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / Respiratory electron transport / Cytoprotection by HMOX1 / respiratory chain complex IV / alpha-beta T cell receptor complex / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway ...Complex IV assembly / TP53 Regulates Metabolic Genes / Respiratory electron transport / Cytoprotection by HMOX1 / respiratory chain complex IV / alpha-beta T cell receptor complex / 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 / T cell receptor complex / 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 / respiratory chain complex I / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / mitochondrial inner membrane / defense response to bacterium / external side of plasma membrane / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / cytosol
Similarity search - Function
NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / : / : / 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 ...NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / : / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / 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
ACETIC ACID / : / : / T-cell receptor alpha chain V region PHDS58 / T-cell receptor beta-2 chain C region / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Cytochrome c oxidase subunit NDUFA4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLuz, J.G. / Huang, M.D. / Garcia, K.C. / Rudolph, M.G. / Teyton, L. / Wilson, I.A.
CitationJournal: J.EXP.MED. / Year: 2002
Title: Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation ...Title: Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions.
Authors: Luz, J.G. / Huang, M.D. / Garcia, K.C. / Rudolph, M.G. / Teyton, L. / Wilson, I.A.
History
DepositionSep 27, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionNov 27, 2002ID: 1JTR
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: 2C T CELL RECEPTOR ALPHA CHAIN
C: 2C T CELL RECEPTOR ALPHA CHAIN
B: 2C T CELL RECEPTOR BETA CHAIN
D: 2C T CELL RECEPTOR BETA CHAIN
H: H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
I: H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
L: MICROGLOBULIN MHC LIGHT CHAIN
M: MICROGLOBULIN MHC LIGHT CHAIN
P: DEV8
Q: DEV8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,30820
Polymers186,14210
Non-polymers3,16610
Water12,160675
1
A: 2C T CELL RECEPTOR ALPHA CHAIN
B: 2C T CELL RECEPTOR BETA CHAIN
H: H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
L: MICROGLOBULIN MHC LIGHT CHAIN
P: DEV8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,55813
Polymers93,0715
Non-polymers2,4878
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 2C T CELL RECEPTOR ALPHA CHAIN
D: 2C T CELL RECEPTOR BETA CHAIN
I: H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN
M: MICROGLOBULIN MHC LIGHT CHAIN
Q: DEV8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7507
Polymers93,0715
Non-polymers6792
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)297.899, 95.942, 84.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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2C T CELL RECEPTOR ... , 2 types, 4 molecules ACBD

#1: Protein 2C T CELL RECEPTOR ALPHA CHAIN / 2C alpha chain


Mass: 22298.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: GenBank: 224220, UniProt: P01738*PLUS
#2: Protein 2C T CELL RECEPTOR BETA CHAIN / 2C beta chain


Mass: 26284.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: GenBank: 1791255, UniProt: P01851*PLUS

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Protein , 2 types, 4 molecules HILM

#3: Protein H-2KBM3 MHC CLASS I MOLECULE HEAVY CHAIN / H-2Kbm3 heavy chain / H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN / K-B ALPHA CHAIN


Mass: 31719.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P01901
#4: Protein MICROGLOBULIN MHC LIGHT CHAIN / microglobulin light chain


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P01887

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Protein/peptide , 1 types, 2 molecules PQ

#5: Protein/peptide DEV8


Mass: 1064.168 Da / Num. of mol.: 2 / Fragment: residues 54-61 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The peptide is naturally found in Mus musculus (Mouse).
References: UniProt: Q62425

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Sugars , 3 types, 6 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: 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


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

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Non-polymers , 3 types, 679 molecules

#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / 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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 277.16 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1M TRIS ACETATE, 12% PEG4000, 18% glycerol, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277.16K

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000
RadiationMonochromator: SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 95548 / % possible obs: 99.5 % / Rsym value: 0.052 / Net I/σ(I): 22.4
Reflection shellResolution: 2.4→2.44 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.453 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→49.39 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43932 / ESU R Free: 0.2997 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.31273 4781 5 %RANDOM
Rwork0.28398 ---
obs0.28543 90694 100 %-
Displacement parametersBiso mean: 47.497 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--2.81 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13089 0 209 675 13973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg1.633
X-RAY DIFFRACTIONr_chiral_restr0.094

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