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- PDB-3p4m: Crystal Structure of H2-Kb in complex with the NP205-LCMV epitope... -

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Basic information

Entry
Database: PDB / ID: 3p4m
TitleCrystal Structure of H2-Kb in complex with the NP205-LCMV epitope YTVKYPNL, an 8-mer peptide from the LCMV
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • NP205-LCMV epitope, YTVKYPNL
KeywordsIMMUNE SYSTEM / H2-Kb / LCMV / TCR / T cell / MHC / viral escape
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / 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 / helical viral capsid ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / 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 / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / learning or memory / hydrolase activity / defense response to bacterium / immune response / ribonucleoprotein complex / lysosomal membrane / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / metal ion binding / cytosol
Similarity search - Function
Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain / 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 ...Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain / 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
ACETYL GROUP / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Nucleoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsGras, S. / Guillonneau, C. / Rossjohn, J.
CitationJournal: To be Published
Title: Crystal Structure of H2-Kb in complex with the NP205-LCMV epitope YTVKYPNL, an 8-mer peptide from the LCMV
Authors: Gras, S. / Guillonneau, C. / Rossjohn, J.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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, K-B alpha chain
B: Beta-2-microglobulin
C: NP205-LCMV epitope, YTVKYPNL
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: NP205-LCMV epitope, YTVKYPNL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6998
Polymers89,6116
Non-polymers882
Water4,342241
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
F: NP205-LCMV epitope, YTVKYPNL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8494
Polymers44,8053
Non-polymers441
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-14 kcal/mol
Surface area19340 Å2
MethodPISA
2
C: NP205-LCMV epitope, YTVKYPNL
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8494
Polymers44,8053
Non-polymers441
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-16 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.730, 90.920, 89.050
Angle α, β, γ (deg.)90.000, 111.090, 90.000
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 / H-2K(B)


Mass: 32102.855 Da / Num. of mol.: 2 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01901
#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 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide NP205-LCMV epitope, YTVKYPNL / Nucleocapsid protein


Mass: 998.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: Q91B91
#4: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M ammonium acetate, 16-24% PEG 3350, 0.1M Na-cacodylate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 32903 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.273 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.5-2.60.2230.2314.49676380137210.28897.9
2.6-2.70.2130.2114.88282326731720.26297.1
2.7-2.80.2110.25.27190282327600.24897.8
2.8-2.90.1790.1656.36306247024010.20497.2
2.9-30.1620.14875268208320230.18397.1
3-40.1030.08511.42919011542110090.10595.4
4-60.0470.04519.115181597855790.05493.3
6-100.0420.03619.45108200518110.04390.3
100.0220.02126.612185684270.02675.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vac

1vac


Resolution: 2.5→19.987 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.39 / σ(F): 0.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.269 3275 9.99 %
Rwork0.1812 --
obs0.1899 32790 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.161 Å2 / ksol: 0.315 e/Å3
Displacement parametersBiso max: 114.57 Å2 / Biso mean: 24.9823 Å2 / Biso min: 1.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.8635 Å20 Å21.0531 Å2
2--5.5265 Å20 Å2
3----4.663 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 6 241 6547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076591
X-RAY DIFFRACTIONf_angle_d1.1198951
X-RAY DIFFRACTIONf_chiral_restr0.076914
X-RAY DIFFRACTIONf_plane_restr0.0051171
X-RAY DIFFRACTIONf_dihedral_angle_d16.4082471
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58920.34593210.24143024334598
2.5892-2.69260.30563490.21222960330997
2.6926-2.81490.32473030.22613045334897
2.8149-2.96280.31093450.20052955330097
2.9628-3.14780.29563280.20032963329196
3.1478-3.38980.29013180.20032946326495
3.3898-3.72890.25873390.16972923326295
3.7289-4.26390.24443180.14962931324994
4.2639-5.35490.19093450.11822898324394
5.3549-19.9880.21593090.14242870317991

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