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- PDB-6h6d: Crystal structures of the murine class I major histocompatibility... -

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Basic information

Entry
Database: PDB / ID: 6h6d
TitleCrystal structures of the murine class I major histocompatibility complex H-2Db in complex with adenovirus-derived peptide Ad10
Components
  • Beta-2-microglobulin
  • Early E1A protein
  • H-2 class I histocompatibility antigen, D-B alpha chain
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 / molecular sequestering activity / 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 ...regulation by virus of viral protein levels in host cell / positive regulation of protein sumoylation / molecular sequestering activity / 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 endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / 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 / peptide binding / 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 / regulation of protein localization / 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 / symbiont-mediated suppression of host gene expression / T cell differentiation in thymus / protein refolding / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein homotetramerization / DNA-binding transcription factor binding / intracellular iron ion homeostasis / amyloid fibril formation / molecular adaptor activity / learning or memory / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / host cell nucleus / positive regulation of cell population proliferation / protein-containing complex binding / regulation of DNA-templated transcription / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / metal ion binding / plasma membrane / 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 / MHC class I-like antigen recognition-like ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Early E1A protein
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: Han, X. / Abualrous, E.T. / Badia-Martines, D. / Sandalova, T. / Sun, R. / van Hall, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Early E1A protein
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Early E1A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,81429
Polymers102,3036
Non-polymers1,51123
Water2,198122
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Early E1A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,14818
Polymers51,1523
Non-polymers99715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-100 kcal/mol
Surface area19480 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: Early E1A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,66611
Polymers51,1523
Non-polymers5148
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-56 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.140, 69.240, 87.160
Angle α, β, γ (deg.)84.20, 86.69, 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
21GLYGLYPROPRODD1 - 2761 - 276
12ILEILEMETMETBB1 - 991 - 99
22ILEILEMETMETEE1 - 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-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 38449.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P01899
#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 Early E1A protein / Early E1A 32 kDa protein


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

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Non-polymers , 4 types, 145 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.74 Å3/Da / Density % sol: 55.03 %
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: Sep 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→20 Å / Num. obs: 42622 / % possible obs: 90 % / Redundancy: 3.5 % / Rsym value: 0.137 / Net I/σ(I): 8.5
Reflection shellResolution: 2.34→2.5 Å / Rmerge(I) obs: 0.64

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Processing

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

1n5a


Resolution: 2.4→19.98 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.822 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.235 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23333 2000 4.9 %RANDOM
Rwork0.19815 ---
obs0.1999 38969 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.314 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20.11 Å20.04 Å2
2--0.27 Å20.32 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.4→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6264 0 79 122 6465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196532
X-RAY DIFFRACTIONr_bond_other_d0.0050.025908
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9468859
X-RAY DIFFRACTIONr_angle_other_deg1.165313639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0965759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88523.591337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.428151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8451550
X-RAY DIFFRACTIONr_chiral_restr0.1010.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217323
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021571
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_it3.9064.5263048
X-RAY DIFFRACTIONr_mcbond_other3.9054.5263047
X-RAY DIFFRACTIONr_mcangle_it6.1636.7693797
X-RAY DIFFRACTIONr_mcangle_other6.1636.7693798
X-RAY DIFFRACTIONr_scbond_it4.4085.0123484
X-RAY DIFFRACTIONr_scbond_other4.4055.0123484
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0357.3125061
X-RAY DIFFRACTIONr_long_range_B_refined9.93335.3957252
X-RAY DIFFRACTIONr_long_range_B_other9.93635.3977252
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A316680.07
12D316680.07
21B116760.08
22E116760.08
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 128 -
Rwork0.314 2498 -
obs--84.76 %

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