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- PDB-3fol: Crystal structure of the Class I MHC Molecule H-2Kwm7 with a Sing... -

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Basic information

Entry
Database: PDB / ID: 3fol
TitleCrystal structure of the Class I MHC Molecule H-2Kwm7 with a Single Self Peptide VNDIFERI
Components
  • 8 residue synthetic peptide
  • Beta-2-microglobulin
  • MHC
KeywordsIMMUNE SYSTEM / Class I MHC / peptide complex / Diabetes-protective Effect / Immune response / Immunoglobulin domain / MHC I / Secreted / Chromosomal protein / DNA-binding / Methylation / Nucleosome core / Nucleus / Phosphoprotein
Function / homology
Function and homology information


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 / 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 ...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 / 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 / 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 / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
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. ...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
MHC / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBrims, D.R. / Qian, J. / Jarchum, I. / Yamada, T. / Mikesh, L. / Palmieri, E. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. ...Brims, D.R. / Qian, J. / Jarchum, I. / Yamada, T. / Mikesh, L. / Palmieri, E. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. / Ramagopal, U.A. / Malashkevich, V.N. / Almo, S.C. / Nathenson, S.G. / DiLorenzo, T.P.
CitationJournal: Int.Immunol. / Year: 2010
Title: Predominant occupation of the class I MHC molecule H-2Kwm7 with a single self-peptide suggests a mechanism for its diabetes-protective effect
Authors: Brims, D.R. / Qian, J. / Jarchum, I. / Mikesh, L. / Palmieri, E. / Ramagopal, U.A. / Malashkevich, V.N. / Chaparro, R.J. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. / Nathenson, ...Authors: Brims, D.R. / Qian, J. / Jarchum, I. / Mikesh, L. / Palmieri, E. / Ramagopal, U.A. / Malashkevich, V.N. / Chaparro, R.J. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. / Nathenson, S.G. / Almo, S.C. / Dilorenzo, T.P.
History
DepositionDec 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC
B: Beta-2-microglobulin
P: 8 residue synthetic peptide


Theoretical massNumber of molelcules
Total (without water)44,3293
Polymers44,3293
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-17 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.393, 66.630, 56.211
Angle α, β, γ (deg.)90.000, 93.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC


Mass: 31487.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: Pet3a / Production host: Escherichia coli (E. coli) / References: UniProt: D2YW38*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 1 / Fragment: IgC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: Pet3a / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide 8 residue synthetic peptide


Mass: 1006.134 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. It is found naturally in mouse.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 200 mM ammonium sulfate, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 27, 2007
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18990 / % possible obs: 97.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.068 / Χ2: 1.072 / Net I/σ(I): 19.169
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.384.20.81914770.856176.4
2.38-2.485.80.76718861.08197.8
2.48-2.597.30.63119531.226199.9
2.59-2.737.50.49219461.1511100
2.73-2.97.40.33519301.14199.9
2.9-3.127.50.19419471.083199.9
3.12-3.447.60.09719361.0481100
3.44-3.937.60.05419520.9421100
3.93-4.957.60.03319581.0781100
4.95-507.40.03520050.987199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
StructureStudiodata collection
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.5→19.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.175 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.79 / SU B: 25.664 / SU ML: 0.27 / SU R Cruickshank DPI: 0.71 / SU Rfree: 0.311 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.709 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.261 757 5 %RANDOM
Rwork0.192 ---
obs0.196 15063 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 92.58 Å2 / Biso mean: 39.517 Å2 / Biso min: 2.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 0 65 3182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213222
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9394377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9335383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55223.353167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.47315539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1061528
X-RAY DIFFRACTIONr_chiral_restr0.0990.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212516
X-RAY DIFFRACTIONr_mcbond_it0.9853.51912
X-RAY DIFFRACTIONr_mcangle_it2.418203095
X-RAY DIFFRACTIONr_scbond_it3.463201310
X-RAY DIFFRACTIONr_scangle_it0.8394.51280
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 51 -
Rwork0.315 1050 -
all-1101 -
obs--99.46 %
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)
13.62132.22242.44611.4921.36732.62640.01910.32690.1367-0.02520.11310.0285-0.10510.3815-0.13220.06240.00070.07050.10520.0240.126421.1576-0.560513.7448
23.32810.45021.6225.52434.40058.62150.3522-0.36840.12680.0571-0.16160.1234-0.4521-0.0669-0.19060.1985-0.09620.1380.2051-0.00290.138318.95892.511232.6636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 274
2X-RAY DIFFRACTION1A275 - 379
3X-RAY DIFFRACTION2B0 - 99

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