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Entry
Database: PDB / ID: 6mp0
TitleCrystal structures of the murine class I major histocompatibility complex H-2Db in complex with the TRP1-M9 peptide
ComponentsTRP1-M9 peptide, Beta-2-microglobulin,H-2 class I histocompatibility antigen, D-B alpha chain, chimeric construct
KeywordsIMMUNE SYSTEM / MHC
Function / homology
Function and homology information


Melanin biosynthesis / melanin biosynthetic process from tyrosine / acetoacetic acid metabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor / tyrosinase activity / melanin metabolic process / positive regulation of melanin biosynthetic process / melanocyte differentiation / melanosome organization / melanosome membrane ...Melanin biosynthesis / melanin biosynthetic process from tyrosine / acetoacetic acid metabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor / tyrosinase activity / melanin metabolic process / positive regulation of melanin biosynthetic process / melanocyte differentiation / melanosome organization / melanosome 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 / regulation of membrane depolarization / pigmentation / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / Neutrophil degranulation / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / clathrin-coated endocytic vesicle membrane / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / 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 assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / positive regulation of immune response / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / melanosome / MHC class II protein complex binding / T cell differentiation in thymus / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome membrane / negative regulation of neuron projection development / antibacterial humoral response / protein refolding / cellular response to lipopolysaccharide / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / learning or memory / endosome membrane / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / innate immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain 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 ...Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain 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 / 5,6-dihydroxyindole-2-carboxylic acid oxidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsClancy-Thompson, E. / Devlin, C.A. / Birnbaum, M.E. / Dougan, S.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P30-CA14051 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)T32CA207021 United States
CitationJournal: Cancer Immunol Res / Year: 2018
Title: Altered Binding of Tumor Antigenic Peptides to MHC Class I Affects CD8+T Cell-Effector Responses.
Authors: Clancy-Thompson, E. / Devlin, C.A. / Tyler, P.M. / Servos, M.M. / Ali, L.R. / Ventre, K.S. / Bhuiyan, M.A. / Bruck, P.T. / Birnbaum, M.E. / Dougan, S.K.
History
DepositionOct 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 11, 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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRP1-M9 peptide, Beta-2-microglobulin,H-2 class I histocompatibility antigen, D-B alpha chain, chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4963
Polymers50,0531
Non-polymers4422
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.061, 98.436, 121.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein TRP1-M9 peptide, Beta-2-microglobulin,H-2 class I histocompatibility antigen, D-B alpha chain, chimeric construct / DHICA oxidase / Brown locus protein / Catalase B / Tyrosinase-related protein 1 / TRP1 / H-2D(B)


Mass: 50053.410 Da / Num. of mol.: 1 / Mutation: Y84A, A9M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tyrp1, Tyrp-1, B2m, H2-D1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P07147, UniProt: P01887, UniProt: P01899, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and ...References: UniProt: P07147, UniProt: P01887, UniProt: P01899, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With another compound as one donor, and incorporation of one atom of oxygen into the other donor
#2: 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.: 2
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 58.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 16% PEG-6000, 200 mM LiCl, and 100 mM Tris-HCl (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→31.682 Å / Num. obs: 40488 / % possible obs: 97.46 % / Redundancy: 11.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1412 / Rrim(I) all: 0.1476 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.071 Å / Mean I/σ(I) obs: 1.58 / CC1/2: 0.527 / % possible all: 78.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDS20170601data reduction
XSCALE20170601data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HUU

4huu


Resolution: 2→31.682 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.62
RfactorNum. reflection% reflection
Rfree0.2283 1989 4.92 %
Rwork0.1954 --
obs0.1971 40439 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→31.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3158 0 28 381 3567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163300
X-RAY DIFFRACTIONf_angle_d1.3944489
X-RAY DIFFRACTIONf_dihedral_angle_d16.8531956
X-RAY DIFFRACTIONf_chiral_restr0.08457
X-RAY DIFFRACTIONf_plane_restr0.009586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.04990.38271080.33842050X-RAY DIFFRACTION74
2.0499-2.10530.27061100.27432573X-RAY DIFFRACTION92
2.1053-2.16720.29851580.24412738X-RAY DIFFRACTION99
2.1672-2.23720.27291330.22022779X-RAY DIFFRACTION100
2.2372-2.31710.27161510.22452776X-RAY DIFFRACTION100
2.3171-2.40980.23521390.22462795X-RAY DIFFRACTION100
2.4098-2.51950.26851310.21652812X-RAY DIFFRACTION100
2.5195-2.65220.30131340.21182828X-RAY DIFFRACTION100
2.6522-2.81830.25141340.21062798X-RAY DIFFRACTION100
2.8183-3.03570.24051550.20112785X-RAY DIFFRACTION100
3.0357-3.34090.22271580.18642844X-RAY DIFFRACTION100
3.3409-3.82370.2011660.172826X-RAY DIFFRACTION100
3.8237-4.81470.16231420.15582867X-RAY DIFFRACTION100
4.8147-31.6860.22811700.1892979X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2570.98460.3743.24810.98620.45720.00440.1312-0.1293-0.1866-0.0616-0.0404-0.028-0.03670.07050.22380.0119-0.01580.22280.0030.191-5.4753-11.446632.3543
23.1112-0.0913-0.37482.72610.14432.7666-0.0230.0909-0.0189-0.0913-0.0354-0.1665-0.00430.1330.06260.1578-0.0274-0.01150.12070.02280.18423.62859.468738.7313
31.49970.5438-0.09794.3684-0.3072.60370.1085-0.161-0.35430.4906-0.22190.14790.74820.07190.07940.3748-0.00060.01850.3699-0.03540.2103-9.8135-17.258352.0432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 2012 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2013 through 2162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2163 through 2277 )

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