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- PDB-1wbz: CRYSTAL STRUCTURES OF MURINE MHC CLASS I H-2 Db AND Kb MOLECULES ... -

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Basic information

Entry
Database: PDB / ID: 1wbz
TitleCRYSTAL STRUCTURES OF MURINE MHC CLASS I H-2 Db AND Kb MOLECULES IN COMPLEX WITH CTL EPITOPES FROM INFLUENZA A VIRUS: IMPLICATIONS FOR TCR REPERTOIRE SELECTION AND IMMUNODOMINANCE
Components
  • BETA-2MICROGLOBULIN
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN PRECURSOR
  • INFLUENZA A PEPTIDE
KeywordsIMMUNE SYSTEM / MHC CLASS I / INFLUENZA PEPTIDE / HA468
Function / homology
Function and homology information


MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / ER-Phagosome pathway ...MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / ER-Phagosome pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / regulation of membrane depolarization / inner ear development / CD8 receptor binding / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular defense response / T cell receptor binding / Neutrophil degranulation / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / 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 erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome membrane / negative regulation of neuron projection development / antibacterial humoral response / protein refolding / protein-folding chaperone binding / cellular response to lipopolysaccharide / early endosome membrane / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / host cell cytoplasm / intracellular iron ion homeostasis / learning or memory / early endosome / defense response to bacterium / defense response to Gram-positive bacterium / immune response / symbiont-mediated suppression of host gene expression / receptor ligand activity / signaling receptor binding / Golgi membrane / external side of plasma membrane / innate immune response / RNA-directed RNA polymerase / lysosomal membrane / nucleotide binding / viral RNA genome replication / RNA-directed RNA polymerase activity / host cell nucleus / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / 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 / : ...Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / 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 / H-2 class I histocompatibility antigen, K-B alpha chain / RNA-directed RNA polymerase catalytic subunit
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
INFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMeijers, R. / Lai, C. / Yang, Y. / Liu, J. / Zhong, W. / Wang, J. / Reinherz, E.L.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structures of Murine Mhc Class I H-2 D(B) and K(B) Molecules in Complex with Ctl Epitopes from Influenza a Virus: Implications for Tcr Repertoire Selection and Immunodominance
Authors: Meijers, R. / Lai, C. / Yang, Y. / Liu, J. / Zhong, W. / Wang, J. / Reinherz, E.L.
History
DepositionNov 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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, K-B ALPHA CHAIN PRECURSOR
B: BETA-2MICROGLOBULIN
C: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN PRECURSOR
D: BETA-2MICROGLOBULIN
P: INFLUENZA A PEPTIDE
Q: INFLUENZA A PEPTIDE


Theoretical massNumber of molelcules
Total (without water)89,0366
Polymers89,0366
Non-polymers00
Water12,412689
1
A: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN PRECURSOR
B: BETA-2MICROGLOBULIN
P: INFLUENZA A PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,5183
Polymers44,5183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN PRECURSOR
D: BETA-2MICROGLOBULIN
Q: INFLUENZA A PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,5183
Polymers44,5183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)89.166, 91.256, 67.183
Angle α, β, γ (deg.)90.00, 111.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN PRECURSOR / H2-KB MHC CLASS I


Mass: 31777.438 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 22-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01901
#2: Protein BETA-2MICROGLOBULIN


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01887
#3: Protein/peptide INFLUENZA A PEPTIDE


Mass: 1036.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: PEPTIDE DERIVED FROM PR8 INFLUENZA A PB1-703 / Source: (synth.) INFLUENZA A VIRUS / References: UniProt: P26144*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)
110 mMTris1droppH8.0
220 mg/mlprotein1drop
310-20 %(w/v)PEG80001reservoir
40.2 Mcalcium acetate1reservoiror magnesium acetate
50.1 Mcacodylate1reservoirpH6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 60662 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.9
Reflection shellResolution: 2→2.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.5 / % possible all: 60
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 60 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KPU

1kpu


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.891 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3221 5 %RANDOM
Rwork0.208 ---
obs0.21 60662 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.07 Å2
2---0.11 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6258 0 0 689 6947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216445
X-RAY DIFFRACTIONr_bond_other_d0.0020.025600
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9288753
X-RAY DIFFRACTIONr_angle_other_deg0.939313052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86223.394330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.758151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1511552
X-RAY DIFFRACTIONr_chiral_restr0.1050.2898
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021367
X-RAY DIFFRACTIONr_nbd_refined0.2180.21240
X-RAY DIFFRACTIONr_nbd_other0.2080.25739
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22979
X-RAY DIFFRACTIONr_nbtor_other0.0960.23820
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2511
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2551.54919
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43626175
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.99633153
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9864.52578
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 151
Rwork0.269 2888
Software
*PLUS
Version: 5.2.0003 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.06 Å / Rfactor Rfree: 0.34 / Rfactor Rwork: 0.258

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