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- PDB-6mp1: Crystal structures of the murine class I major histocompatibility... -

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Basic information

Entry
Database: PDB / ID: 6mp1
TitleCrystal structures of the murine class I major histocompatibility complex H-2Db in complex with the mutant TRP1-K8 peptide
ComponentsTRP1-K8 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 / 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 / acetoacetic acid metabolic process / melanin metabolic process / positive regulation of melanin biosynthetic process / tyrosinase activity / melanocyte differentiation / melanosome membrane / melanosome organization ...Melanin biosynthesis / melanin biosynthetic process from tyrosine / 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 / acetoacetic acid metabolic process / melanin metabolic process / positive regulation of melanin biosynthetic process / tyrosinase activity / melanocyte differentiation / melanosome membrane / melanosome organization / 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 / pigmentation / intracellular vesicle / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / clathrin-coated endocytic vesicle membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / melanosome / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / metal ion binding / plasma membrane / cytoplasm / 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 / MHC class I alpha chain, alpha1 alpha2 domains ...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 / Immunoglobulins / Immunoglobulin-like fold / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.211 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRP1-K8 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)50,4623
Polymers50,0191
Non-polymers4422
Water1,04558
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)52.569, 68.329, 117.787
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRP1-K8 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: 50019.418 Da / Num. of mol.: 1 / Mutation: Y84A, Y8K, 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.: 58 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 30% PEG-1500, 100 mM MIB buffer, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.211→48.0162 Å / Num. obs: 21851 / % possible obs: 99.43 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1137 / Rrim(I) all: 0.1202 / Net I/σ(I): 13.82
Reflection shellResolution: 2.211→2.29 Å / Rmerge(I) obs: 1.711 / Mean I/σ(I) obs: 0.89 / CC1/2: 0.406 / Rrim(I) all: 1.825

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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: 2.211→48.005 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.21
RfactorNum. reflection% reflection
Rfree0.2442 1129 5.19 %
Rwork0.2092 --
obs0.2111 21761 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.211→48.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 28 58 3225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033263
X-RAY DIFFRACTIONf_angle_d0.6414432
X-RAY DIFFRACTIONf_dihedral_angle_d12.7561936
X-RAY DIFFRACTIONf_chiral_restr0.044453
X-RAY DIFFRACTIONf_plane_restr0.004576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2106-2.31120.35811170.30712420X-RAY DIFFRACTION95
2.3112-2.43310.37751260.28442573X-RAY DIFFRACTION100
2.4331-2.58550.30191270.27192546X-RAY DIFFRACTION100
2.5855-2.78510.30231540.27142578X-RAY DIFFRACTION100
2.7851-3.06540.32211490.25852560X-RAY DIFFRACTION100
3.0654-3.50880.27051420.2332599X-RAY DIFFRACTION100
3.5088-4.42030.21691520.17252609X-RAY DIFFRACTION100
4.4203-48.01620.19531620.17562747X-RAY DIFFRACTION100
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)
17.29160.7031-1.83390.78840.17711.1083-0.02640.63810.139-0.07340.0605-0.10920.0635-0.138-0.05390.39680.04850.0240.4070.04060.455117.60982.8338-27.5459
26.37974.0083-5.25584.2412-3.29985.57780.08230.40730.5306-0.03250.08640.1995-0.2637-0.2239-0.25850.42640.0776-0.00350.4628-0.01870.477823.5795.5235-27.5501
35.42990.88760.6741.2557-0.04870.0658-0.0080.4878-0.0887-0.33980.05260.05840.19640.03760.03990.5610.0479-0.01240.375-0.04240.41988.94930.4337-31.1272
41.7114-0.51130.49684.2374-1.67473.05440.054-0.11270.0999-0.0935-0.04220.04750.01080.01710.00060.3811-0.00340.0730.365-0.04490.4353-1.75330.4267-18.478
58.7824-3.5507-3.65552.28741.41022.73430.26050.21330.1098-0.1838-0.1779-0.1075-0.0543-0.1536-0.12410.4434-0.0302-0.05420.3638-0.06830.35617.75510.0663-42.0072
68.9288-5.8448-1.76688.16822.05444.86450.07530.152-0.45610.0862-0.06050.22870.4227-0.1395-0.0430.3830.0210.00090.45270.02850.314519.9301-10.4701-47.4543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 1041 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1042 through 1094 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1095 through 2013 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2014 through 2162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2163 through 2197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 2198 through 2276 )

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