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

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Basic information

Entry
Database: PDB / ID: 3fon
TitleCrystal structure of the Class I MHC Molecule H-2Kwm7 with a Single Self Peptide VNDIFEAI
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC
  • Peptide
KeywordsIMMUNE SYSTEM / Class I MHC / peptide complex / Diabetes-protective Effect / Immune response / Immunoglobulin domain / MHC I / Secreted
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / regulation of membrane depolarization / cellular defense response / Neutrophil degranulation ...antigen processing and presentation of peptide antigen via MHC class I / 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 / regulation of membrane depolarization / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å
AuthorsMalashkevich, V.N. / Qian, J. / Jarchum, I. / Yamada, T. / Mikesh, L. / Palmieri, E. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. ...Malashkevich, V.N. / Qian, J. / Jarchum, I. / Yamada, T. / Mikesh, L. / Palmieri, E. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. / Ramagopal, U.A. / Brims, D.R. / 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
Revision 2.0Feb 5, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC
B: Beta-2-microglobulin
P: Peptide
C: MHC
D: Beta-2-microglobulin
E: Peptide


Theoretical massNumber of molelcules
Total (without water)88,4856
Polymers88,4856
Non-polymers00
Water9,386521
1
A: MHC
B: Beta-2-microglobulin
P: Peptide


Theoretical massNumber of molelcules
Total (without water)44,2433
Polymers44,2433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-14 kcal/mol
Surface area19030 Å2
MethodPISA
2
C: MHC
D: Beta-2-microglobulin
E: Peptide


Theoretical massNumber of molelcules
Total (without water)44,2433
Polymers44,2433
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-16 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.607, 68.002, 149.920
Angle α, β, γ (deg.)90.000, 105.540, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 1 / Auth seq-ID: -99999 - 99999 / Label seq-ID: -99999 - 99999

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CD
12BB
22DE
13CC
23EF

NCS ensembles :
ID
1
2
3

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Components

#1: Protein MHC


Mass: 31487.088 Da / Num. of mol.: 2 / Fragment: MHC
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 / Beta-2 microglobulin


Mass: 11835.555 Da / Num. of mol.: 2 / 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 Peptide /


Mass: 920.018 Da / Num. of mol.: 2 / Fragment: Peptide / Source method: obtained synthetically / Details: Peptide synthesis / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3000, 100 mM HEPES, pH 7.5, 200 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 64629 / % possible obs: 99 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.063 / Χ2: 1.136 / Net I/σ(I): 18.964
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.04-2.113.40.47859441.143191.7
2.11-2.23.70.38765181.1961100
2.2-2.33.70.27964911.144199.9
2.3-2.423.70.22764721.2231100
2.42-2.573.70.1664961.172199.9
2.57-2.773.70.11264901.1161100
2.77-3.053.80.07665191.1461100
3.05-3.493.70.05165741.061100
3.49-4.393.60.04265231.075199.7
4.39-503.60.03166021.09198.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.03→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.26 / WRfactor Rwork: 0.221 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.734 / SU B: 9.23 / SU ML: 0.12 / SU R Cruickshank DPI: 0.197 / SU Rfree: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3264 5.1 %RANDOM
Rwork0.213 ---
obs0.215 64497 99.41 %-
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: 93.68 Å2 / Biso mean: 27.276 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.01 Å2
2---0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.03→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6226 0 0 521 6747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216446
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.9398763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70223.363333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.775151073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9461555
X-RAY DIFFRACTIONr_chiral_restr0.1280.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215049
X-RAY DIFFRACTIONr_mcbond_it1.2253.53831
X-RAY DIFFRACTIONr_mcangle_it2.962206202
X-RAY DIFFRACTIONr_scbond_it4.358202615
X-RAY DIFFRACTIONr_scangle_it1.4494.52556
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2206TIGHT POSITIONAL0.070.05
12C2206TIGHT THERMAL0.160.5
21B821TIGHT POSITIONAL0.10.05
22D821TIGHT THERMAL0.170.5
31P65TIGHT POSITIONAL0.030.05
32E65TIGHT THERMAL0.190.5
LS refinement shellResolution: 2.032→2.084 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 217 -
Rwork0.285 4334 -
all-4551 -
obs--95.75 %
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)
10.64150.0609-0.26970.8593-0.33791.3696-0.108-0.04450.00580.06820.10740.0616-0.0408-0.00150.00060.02930.0199-0.00320.0254-0.00620.034515.2154-0.21739.8309
21.51730.57260.582.0738-0.81422.074-0.13050.12160.19570.0706-0.0468-0.1957-0.15630.39840.17730.0203-0.0242-0.0330.09550.01610.067133.57550.38275.0697
30.6318-0.1204-0.1780.94140.81711.4846-0.09450.05110.0342-0.10450.09-0.0419-0.13480.03260.00440.0346-0.0196-0.00690.02390.01060.035416.513829.936762.3378
41.3296-0.7270.35911.85350.99472.4175-0.1193-0.10430.1657-0.0828-0.07950.1785-0.1903-0.39980.19880.02660.0294-0.03980.0879-0.03230.0764-1.736530.843767.0094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 274
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C1 - 274
4X-RAY DIFFRACTION3C275 - 795
5X-RAY DIFFRACTION4D0 - 99

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