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- PDB-6h6h: Crystal structures of the murine class I major histocompatibility... -

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Basic information

Entry
Database: PDB / ID: 6h6h
TitleCrystal structures of the murine class I major histocompatibility complex H-2Dbm13 in complex with adenovirus-derived peptide Ad10
Components
  • Beta-2-microglobulin
  • H-2D cell surface glycoprotein
  • SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
KeywordsIMMUNE SYSTEM / MHC class I / adenovirus
Function / homology
Function and homology information


regulation by virus of viral protein levels in host cell / positive regulation of protein sumoylation / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation of peptide antigen via MHC class I ...regulation by virus of viral protein levels in host cell / positive regulation of protein sumoylation / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation of peptide antigen via MHC class I / molecular sequestering activity / cellular defense response / Neutrophil degranulation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / MHC class I protein complex / 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 / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / regulation of protein localization / negative regulation of neuron projection development / protein refolding / protein homotetramerization / molecular adaptor activity / DNA-binding transcription factor binding / symbiont-mediated perturbation of host ubiquitin-like protein modification / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / external side of plasma membrane / positive regulation of cell population proliferation / regulation of DNA-templated transcription / host cell nucleus / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / zinc ion binding / cytosol
Similarity search - Function
Adenovirus early E1A protein / Early E1A protein / 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 / : ...Adenovirus early E1A protein / Early E1A protein / 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
Beta-2-microglobulin / Early E1A protein / H-2D cell surface glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
unidentified adenovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAchour, A. / Sandalova, T. / Han, X.
CitationJournal: to be published
Title: Crystal structures of H-2Db and H-2Dbm13 with cancer-associated Ad 10 peptide reveal that subtle changes in the peptide environment impact thermostability and alloreactivity
Authors: Abualrous, E.T. / Han, X. / Badia-Martines, D. / Sun, R. / van Hall, T. / Sandalova, T. / Ossendorp, F. / Achour, A.
History
DepositionJul 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2D cell surface glycoprotein
D: H-2D cell surface glycoprotein
B: Beta-2-microglobulin
E: Beta-2-microglobulin
C: SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
F: SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,96223
Polymers102,3376
Non-polymers1,62517
Water3,513195
1
A: H-2D cell surface glycoprotein
B: Beta-2-microglobulin
C: SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,31315
Polymers51,1683
Non-polymers1,14512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-132 kcal/mol
Surface area19520 Å2
MethodPISA
2
D: H-2D cell surface glycoprotein
E: Beta-2-microglobulin
F: SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6498
Polymers51,1683
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-100 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.410, 70.270, 87.050
Angle α, β, γ (deg.)83.98, 86.90, 81.75
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPRODB1 - 2761 - 276
12ILEILEMETMETBC1 - 991 - 99
22ILEILEMETMETED1 - 991 - 99

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein H-2D cell surface glycoprotein


Mass: 38466.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1, H-2D, H2-L / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q31167
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01887

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE


Mass: 998.045 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified adenovirus / References: UniProt: P03255*PLUS

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Non-polymers , 3 types, 212 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1.8M ammonium sulphate, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 42580 / % possible obs: 97.1 % / Redundancy: 3.1 % / Rsym value: 0.121 / Net I/σ(I): 7
Reflection shellResolution: 2.4→2.57 Å / Rsym value: 0.57

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N5A

1n5a


Resolution: 2.4→19.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.329 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.249 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24869 2133 5.1 %RANDOM
Rwork0.20012 ---
obs0.2026 39771 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.06 Å2-0.04 Å2
2---0.22 Å20.28 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 87 195 6548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196540
X-RAY DIFFRACTIONr_bond_other_d0.0040.025839
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9498888
X-RAY DIFFRACTIONr_angle_other_deg1.11313481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74223.728338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.054151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2781548
X-RAY DIFFRACTIONr_chiral_restr0.0840.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217326
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021566
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1245.2063046
X-RAY DIFFRACTIONr_mcbond_other3.1245.2063045
X-RAY DIFFRACTIONr_mcangle_it5.0227.7923794
X-RAY DIFFRACTIONr_mcangle_other5.0217.7923795
X-RAY DIFFRACTIONr_scbond_it3.4985.6673494
X-RAY DIFFRACTIONr_scbond_other3.4975.6673494
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.688.3355094
X-RAY DIFFRACTIONr_long_range_B_refined8.6840.5256992
X-RAY DIFFRACTIONr_long_range_B_other8.6840.5286991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A31012
12D31012
21B11650
22E11650
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 158 -
Rwork0.299 2895 -
obs--96.83 %

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