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

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Basic information

Entry
Database: PDB / ID: 6lam
TitleCrystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylethanolamine
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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex ...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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / recycling endosome membrane / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / structural molecule activity / cell surface / Golgi apparatus / protein homodimerization activity / extracellular region / metal ion binding / 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: 1.8 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
DepositionNov 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 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 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Revision 1.3Oct 30, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,78541
Polymers86,8384
Non-polymers2,94737
Water9,044502
1
A: MHC class I antigen
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,62316
Polymers43,4192
Non-polymers1,20414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MHC class I antigen
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,16225
Polymers43,4192
Non-polymers1,74323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)251.879, 46.729, 84.983
Angle α, β, γ (deg.)90.000, 90.801, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 31687.727 Da / Num. of mol.: 2 / Mutation: C167S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: Mamu-B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: A0A1E1GJG5
#2: Protein Beta-2-microglobulin


Mass: 11731.157 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q6V7J5

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Non-polymers , 6 types, 539 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-EKG / (2R)-2,3-dihydroxypropyl hexadecanoate


Mass: 330.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H38O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.15 / Details: Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%

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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: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79977133822→50 Å / Num. obs: 91433 / % possible obs: 99.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 22.09 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 46.34
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.254 / Num. unique obs: 4423 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zfz

4zfz


Resolution: 1.8→40.09 Å / SU ML: 0.1878 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.1969 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2287 4463 4.88 %
Rwork0.1914 86953 -
obs0.1932 91416 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.69 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6122 0 173 502 6797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00746618
X-RAY DIFFRACTIONf_angle_d0.93678941
X-RAY DIFFRACTIONf_chiral_restr0.0551881
X-RAY DIFFRACTIONf_plane_restr0.00511191
X-RAY DIFFRACTIONf_dihedral_angle_d25.07252506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.29021370.23872687X-RAY DIFFRACTION94.45
1.82-1.840.26991370.22622857X-RAY DIFFRACTION98.29
1.84-1.860.24381290.21342939X-RAY DIFFRACTION98.59
1.86-1.890.25781350.22172869X-RAY DIFFRACTION98.49
1.89-1.910.28081530.21592843X-RAY DIFFRACTION98.62
1.91-1.940.26491710.21442868X-RAY DIFFRACTION98.7
1.94-1.970.2391580.20972807X-RAY DIFFRACTION98.7
1.97-20.26831420.20972858X-RAY DIFFRACTION98.65
2-2.030.25771270.20982957X-RAY DIFFRACTION98.62
2.03-2.060.26721430.21322848X-RAY DIFFRACTION98.94
2.06-2.10.26151590.21232873X-RAY DIFFRACTION98.83
2.1-2.130.22891410.21862901X-RAY DIFFRACTION99.12
2.13-2.170.24771710.21042843X-RAY DIFFRACTION99.08
2.17-2.220.22291250.20452962X-RAY DIFFRACTION99.13
2.22-2.270.25531440.21042826X-RAY DIFFRACTION99.17
2.27-2.320.27851440.20292945X-RAY DIFFRACTION99.23
2.32-2.380.27981350.21382919X-RAY DIFFRACTION99.35
2.38-2.440.27571580.2122880X-RAY DIFFRACTION99.28
2.44-2.510.25041780.20622876X-RAY DIFFRACTION99.51
2.51-2.60.25871570.21372914X-RAY DIFFRACTION99.55
2.6-2.690.24931470.20362898X-RAY DIFFRACTION99.54
2.69-2.80.22281430.2112920X-RAY DIFFRACTION99.64
2.8-2.920.24471800.20432941X-RAY DIFFRACTION99.71
2.92-3.080.22481550.20112892X-RAY DIFFRACTION99.71
3.08-3.270.23281460.1922949X-RAY DIFFRACTION99.81
3.27-3.520.23941390.19032954X-RAY DIFFRACTION99.97
3.52-3.880.2161550.17962991X-RAY DIFFRACTION99.94
3.88-4.440.19691510.15172941X-RAY DIFFRACTION99.77
4.44-5.590.14831490.14542989X-RAY DIFFRACTION99.78
5.59-40.090.1921540.17083006X-RAY DIFFRACTION96.67

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