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- PDB-6a97: Crystal structure of MHC-like MILL2 -

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Basic information

Entry
Database: PDB / ID: 6a97
TitleCrystal structure of MHC-like MILL2
Components
  • Beta-2-microglobulin
  • MHC I-like leukocyte 2 long form
KeywordsIMMUNE SYSTEM / MHC-like
Function / homology
Function and homology information


: / immune response-activating cell surface receptor signaling pathway / natural killer cell lectin-like receptor binding / negative regulation of defense response to virus by host / gamma-delta T cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling ...: / immune response-activating cell surface receptor signaling pathway / natural killer cell lectin-like receptor binding / negative regulation of defense response to virus by host / gamma-delta T cell activation / 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 / cellular defense response / response to retinoic acid / Neutrophil degranulation / 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 / 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 / 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 / response to heat / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / response to oxidative stress / amyloid fibril formation / learning or memory / lysosomal membrane / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
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 ...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 / Mainly Beta
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I-like protein MILL2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.148 Å
AuthorsKajikawa, M. / Ose, T. / Maenaka, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)20057020 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Structure of MHC class I-like MILL2 reveals heparan-sulfate binding and interdomain flexibility.
Authors: Kajikawa, M. / Ose, T. / Fukunaga, Y. / Okabe, Y. / Matsumoto, N. / Yonezawa, K. / Shimizu, N. / Kollnberger, S. / Kasahara, M. / Maenaka, K.
History
DepositionJul 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC I-like leukocyte 2 long form
B: Beta-2-microglobulin
C: MHC I-like leukocyte 2 long form
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6245
Polymers89,5284
Non-polymers961
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-35 kcal/mol
Surface area34670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.633, 93.497, 138.123
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 MHC I-like leukocyte 2 long form


Mass: 32972.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mill2 / Production host: unidentified plasmid (others) / References: UniProt: Q8HWE5
#2: Protein Beta-2-microglobulin


Mass: 11791.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: unidentified plasmid (others) / References: UniProt: P01887
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M BIS-Tris propane HCl, 20% (w/v) polyethylene glycol 3350, 0.2 M sodium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.148→50 Å / Num. obs: 63953 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.085 / Net I/σ(I): 36.4
Reflection shellResolution: 2.148→2.19 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3168 / CC1/2: 0.622 / Rpim(I) all: 0.519 / Rrim(I) all: 1.313 / Χ2: 0.831 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.148→44.816 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 3199 5.01 %
Rwork0.2129 --
obs0.2145 63875 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.148→44.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5387 0 5 204 5596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045522
X-RAY DIFFRACTIONf_angle_d0.8347487
X-RAY DIFFRACTIONf_dihedral_angle_d14.222004
X-RAY DIFFRACTIONf_chiral_restr0.031845
X-RAY DIFFRACTIONf_plane_restr0.003955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1478-2.17980.33041340.28142531X-RAY DIFFRACTION98
2.1798-2.21390.28081140.27292612X-RAY DIFFRACTION100
2.2139-2.25020.29081450.2622614X-RAY DIFFRACTION100
2.2502-2.2890.30381390.25292639X-RAY DIFFRACTION100
2.289-2.33060.30451300.24932613X-RAY DIFFRACTION100
2.3306-2.37540.29271480.24312589X-RAY DIFFRACTION100
2.3754-2.42390.281400.2542618X-RAY DIFFRACTION100
2.4239-2.47660.30711390.25332607X-RAY DIFFRACTION100
2.4766-2.53420.30451470.23992601X-RAY DIFFRACTION100
2.5342-2.59760.28011430.23582638X-RAY DIFFRACTION100
2.5976-2.66780.26271250.23712626X-RAY DIFFRACTION100
2.6678-2.74630.29621380.25162626X-RAY DIFFRACTION100
2.7463-2.83490.26711440.24832620X-RAY DIFFRACTION100
2.8349-2.93620.2721310.25652657X-RAY DIFFRACTION100
2.9362-3.05380.26061300.24862635X-RAY DIFFRACTION100
3.0538-3.19270.28761320.24022644X-RAY DIFFRACTION100
3.1927-3.3610.21491440.22392644X-RAY DIFFRACTION100
3.361-3.57150.22411440.21932648X-RAY DIFFRACTION100
3.5715-3.84710.22741460.22649X-RAY DIFFRACTION100
3.8471-4.2340.24051600.18222653X-RAY DIFFRACTION100
4.234-4.8460.19521450.16042678X-RAY DIFFRACTION100
4.846-6.10310.19751420.1842736X-RAY DIFFRACTION100
6.1031-44.82620.26691390.20732798X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 59.3493 Å / Origin y: 25.4805 Å / Origin z: -29.2367 Å
111213212223313233
T0.2696 Å2-0.0175 Å2-0.0162 Å2-0.3378 Å2-0.0475 Å2--0.3606 Å2
L0.5867 °2-0.1158 °20.1731 °2-0.5596 °2-0.6637 °2--1.3433 °2
S0.0624 Å °0.1199 Å °-0.0134 Å °-0.1893 Å °0.0451 Å °-0.0118 Å °0.2756 Å °0.0049 Å °-0.1071 Å °
Refinement TLS groupSelection details: all

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