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- PDB-3l3h: X-ray crystal structure of the F6A mutant of influenza A acid pol... -

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Basic information

Entry
Database: PDB / ID: 3l3h
TitleX-ray crystal structure of the F6A mutant of influenza A acid polymerase epitope PA224 bound to murine H2-Db MHC
Components
  • 10-mer peptide from Polymerase acidic protein
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsIMMUNE SYSTEM / Animals Antigens / Viral Epitopes / T-Lymphocyte Histocompatibility Antigens / Mice Antigen / T-Cell / T-Lymphocytes / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain / Secreted
Function / homology
Function and homology information


TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / positive regulation of natural killer cell mediated cytotoxicity / cap snatching / regulation of membrane depolarization / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / endonuclease activity / cellular response to lipopolysaccharide / intracellular iron ion homeostasis
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 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 ...Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 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 / Polymerase acidic protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWelland, A. / Clements, C.S. / Dunstone, M.A. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Constraints within major histocompatibility complex class I restricted peptides: presentation and consequences for T-cell recognition
Authors: Theodossis, A. / Guillonneau, C. / Welland, A. / Ely, L.K. / Clements, C.S. / Williamson, N.A. / Webb, A.I. / Wilce, J.A. / Mulder, R.J. / Dunstone, M.A. / Doherty, P.C. / McCluskey, J. / ...Authors: Theodossis, A. / Guillonneau, C. / Welland, A. / Ely, L.K. / Clements, C.S. / Williamson, N.A. / Webb, A.I. / Wilce, J.A. / Mulder, R.J. / Dunstone, M.A. / Doherty, P.C. / McCluskey, J. / Purcell, A.W. / Turner, S.J. / Rossjohn, J.
History
DepositionDec 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: 10-mer peptide from Polymerase acidic protein


Theoretical massNumber of molelcules
Total (without water)44,8453
Polymers44,8453
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-16 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.068, 56.068, 275.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32030.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11704.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide 10-mer peptide from Polymerase acidic protein / 10-mer peptide from RNA-directed RNA polymerase subunit P2


Mass: 1110.199 Da / Num. of mol.: 1 / Mutation: F6A / Source method: obtained synthetically / Details: Fmoc-peptide synthesis / References: UniProt: Q17TI0
#4: Water ChemComp-HOH / water / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M citrate, 0.2M ammonium acetate, 25% PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.51478 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.51478 Å / Relative weight: 1
ReflectionResolution: 2.7→28 Å / Num. all: 12799 / Num. obs: 12799 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 18.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 5.1 / % possible all: 98

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CC5

3cc5


Resolution: 2.7→28 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.854 / SU B: 27.379 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28409 1268 9.9 %RANDOM
Rwork0.22031 ---
all0.22031 12799 --
obs0.22673 11531 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.7→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 0 122 3282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213256
X-RAY DIFFRACTIONr_angle_refined_deg0.8881.9384423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9745381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3323.588170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64615537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8791525
X-RAY DIFFRACTIONr_chiral_restr0.060.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022558
X-RAY DIFFRACTIONr_nbd_refined0.1650.21382
X-RAY DIFFRACTIONr_nbtor_refined0.2910.22144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.26
X-RAY DIFFRACTIONr_mcbond_it0.1411.51985
X-RAY DIFFRACTIONr_mcangle_it0.25523101
X-RAY DIFFRACTIONr_scbond_it0.30731504
X-RAY DIFFRACTIONr_scangle_it0.5254.51322
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 80 -
Rwork0.252 819 -
obs--98.25 %
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)
11.4932-0.3943-0.99772.22331.16544.9406-0.13040.0625-0.00160.02570.02370.1931-0.0742-0.01980.1067-0.1211-0.0106-0.017-0.14540.0563-0.0314-30.2276-15.2614-30.7625
23.1036-1.6521-0.37623.20991.21581.4224-0.1706-0.32940.25960.28820.4219-0.40640.00120.547-0.25130.02150.047-0.01070.0564-0.0944-0.0776-10.4244-34.7001-5.9246
31.45511.1265-0.29755.7972-3.17083.9198-0.06250.1145-0.0754-0.00740.04590.1920.0383-0.25860.0166-0.08260.05410.041-0.0685-0.0598-0.0664-26.5397-41.5141-20.6199
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B1 - 99

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