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- PDB-3c9n: Crystal Structure of a SARS Corona Virus Derived Peptide Bound to... -

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Basic information

Entry
Database: PDB / ID: 3c9n
TitleCrystal Structure of a SARS Corona Virus Derived Peptide Bound to the Human Major Histocompatibility Complex Class I molecule HLA-B*1501
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-15 alpha chain
  • Peptide antigen
KeywordsIMMUNE SYSTEM / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I / MHC-I / HLA-B*1501 / SARS / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Polymorphism / Transmembrane / Ubl conjugation / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / defense response / 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 / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsRoder, G.A. / Kristensen, O. / Kastrup, J.S. / Buus, S. / Gajhede, M.
CitationJournal: ACTA CRYSTALLOGR.,SECT.F / Year: 2008
Title: Structure of a SARS coronavirus-derived peptide bound to the human major histocompatibility complex class I molecule HLA-B*1501.
Authors: Roder, G. / Kristensen, O. / Kastrup, J.S. / Buus, S. / Gajhede, M.
History
DepositionFeb 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HLA class I histocompatibility antigen, B-15 alpha chain
B: Beta-2-microglobulin
C: Peptide antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1935
Polymers44,7613
Non-polymers4332
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.658, 81.713, 109.391
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, B-15 alpha chain / MHC class I antigen B*15


Mass: 31958.195 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30464, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Peptide antigen


Mass: 1054.174 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide derived from SARS Coronavirus; Produced using Fmoc chemistry

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Non-polymers , 3 types, 357 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growTemperature: 273 K / pH: 7.5
Details: 0.2M Magnesium chloride hexahydrate, 0.1M HEPES sodium, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K, pH 7.50

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.90718
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 20, 2006
RadiationMonochromator: BENT CRYSTAL, HORIZONTALLY FOCUSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90718 Å / Relative weight: 1
ReflectionResolution: 1.87→18.29 Å / Num. obs: 38220 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 10.47 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.7
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.97 Å40.83 Å
Translation1.97 Å40.83 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XR9

1xr9


Resolution: 1.87→18.29 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.956 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1910 5 %RANDOM
Rwork0.188 ---
obs0.19 36303 99.8 %-
all-38305 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.39 Å2
Refine analyzeLuzzati coordinate error obs: 0.204 Å
Refinement stepCycle: LAST / Resolution: 1.87→18.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 28 357 3569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213308
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9394500
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4245395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88923.352179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56315537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8211531
X-RAY DIFFRACTIONr_chiral_restr0.1080.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022609
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.21510
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22185
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2350
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1791.52001
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.74823143
X-RAY DIFFRACTIONr_scbond_it2.58231530
X-RAY DIFFRACTIONr_scangle_it4.094.51350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 150 -
Rwork0.262 2637 -
obs--100 %

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