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- PDB-6lt6: Crystal structure of rhesus macaque MHC class I molecule Mamu-B*0... -

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Basic information

Entry
Database: PDB / ID: 6lt6
TitleCrystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with lysophosphatidylcholine
Components
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC class I protein / complex / lysophospholipid
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation ...antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / structural molecule activity / Golgi apparatus / cell surface / protein homodimerization activity / extracellular region / cytosol
Similarity search - Function
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 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
(2R)-2,3-dihydroxypropyl hexadecanoate / B protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsShima, Y. / Morita, D.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K07172 Japan
Japan Society for the Promotion of Science (JSPS)17H05791 Japan
Japan Society for the Promotion of Science (JSPS)18K19563 Japan
Japan Society for the Promotion of Science (JSPS)18H02852 Japan
Japan Society for the Promotion of Science (JSPS)19H04805 Japan
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structures of lysophospholipid-bound MHC class I molecules.
Authors: Shima, Y. / Morita, D. / Mizutani, T. / Mori, N. / Mikami, B. / Sugita, M.
History
DepositionJan 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,48612
Polymers43,6362
Non-polymers85010
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-8 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.451, 81.028, 106.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen / MHC-class I protein


Mass: 31905.137 Da / Num. of mol.: 1 / Mutation: R128E, K177E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: Mamu-B, B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: B2ZHY7
#2: Protein Beta-2-microglobulin


Mass: 11731.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: Q6V7J5

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Non-polymers , 4 types, 218 molecules

#3: Chemical ChemComp-EKG / (2R)-2,3-dihydroxypropyl hexadecanoate


Mass: 330.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H38O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Bis-Tris propane, 0.2M Sodium malonate dibasic monohydrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 25511 / % possible obs: 96 % / Redundancy: 7.7 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 32.3
Reflection shellResolution: 2.15→2.19 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.83 / Num. unique obs: 1228

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IWG

6iwg


Resolution: 2.15→45.19 Å / SU ML: 0.2932 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.959 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2315 1248 4.95 %
Rwork0.1819 23968 -
obs0.1844 25216 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.8 Å2
Refinement stepCycle: LAST / Resolution: 2.15→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 56 208 3346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083278
X-RAY DIFFRACTIONf_angle_d0.95674440
X-RAY DIFFRACTIONf_chiral_restr0.0524434
X-RAY DIFFRACTIONf_plane_restr0.0057592
X-RAY DIFFRACTIONf_dihedral_angle_d27.16971235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.240.33461170.2272565X-RAY DIFFRACTION93.91
2.24-2.340.29851240.21722551X-RAY DIFFRACTION92.85
2.34-2.460.23661350.20752510X-RAY DIFFRACTION92.45
2.46-2.620.31041380.21242550X-RAY DIFFRACTION93.14
2.62-2.820.26671360.19852585X-RAY DIFFRACTION94.71
2.82-3.10.261300.19822720X-RAY DIFFRACTION98.28
3.1-3.550.22611620.18512751X-RAY DIFFRACTION99.62
3.55-4.470.20181460.15222812X-RAY DIFFRACTION99.9
4.47-45.190.19671600.16742924X-RAY DIFFRACTION99.81

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