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- PDB-3to2: Structure of HLA-A*0201 complexed with peptide Md3-C9 derived fro... -

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Basic information

Entry
Database: PDB / ID: 3to2
TitleStructure of HLA-A*0201 complexed with peptide Md3-C9 derived from a clustering region of restricted cytotoxic T lymphocyte epitope from SARS-CoV M protein
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Md3-C9 peptide derived from Membrane glycoprotein
KeywordsIMMUNE SYSTEM / presentation / HLA / CTL epitope
Function / homology
Function and homology information


Maturation of protein M / Translation of Structural Proteins / Virion Assembly and Release / antigen processing and presentation / host cell Golgi membrane / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding ...Maturation of protein M / Translation of Structural Proteins / Virion Assembly and Release / antigen processing and presentation / host cell Golgi membrane / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / 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 / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / ER to Golgi transport vesicle membrane / 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 / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / SARS-CoV-1 activates/modulates innate immune responses / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / structural constituent of virion / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / focal adhesion / virus-mediated perturbation of host defense response / viral envelope / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / virion membrane / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
M matrix/glycoprotein, SARS-CoV-like / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile. / 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 ...M matrix/glycoprotein, SARS-CoV-like / M matrix/glycoprotein, coronavirus / Coronavirus M matrix/glycoprotein / Coronavirus membrane (Cov-M) protein profile. / 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
Membrane protein / Beta-2-microglobulin / HLA class I antigen / Membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
SARS coronavirus TJF
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiu, J. / Qi, J. / Gao, F. / Yan, J. / Gao, G.F.
CitationJournal: Sci.Technology Rev. / Year: 2011
Title: Functional and Structural Definition of a Clustering Region of HLA-A2-restricted Cytotoxic T Lymphocyte Epitopes
Authors: Liu, J. / Qi, J. / Gao, F. / Yan, J. / Gao, G.F.
History
DepositionSep 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Md3-C9 peptide derived from Membrane glycoprotein


Theoretical massNumber of molelcules
Total (without water)44,6403
Polymers44,6403
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-25 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.459, 147.459, 49.903
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein MHC class I antigen / HLA-A*0201 / Major histocompatibility complex / class I / A


Mass: 31854.203 Da / Num. of mol.: 1 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Human / Gene: HLA / Production host: Escherichia coli (E. coli) / References: UniProt: Q53Z42
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Md3-C9 peptide derived from Membrane glycoprotein


Mass: 906.142 Da / Num. of mol.: 1 / Fragment: UNP residues 61-69 / Source method: obtained synthetically / Details: This sequence is synthesized. / Source: (synth.) SARS coronavirus TJF / References: UniProt: Q692E0, UniProt: P59596*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Ammonium acetate, 0.1M BIS-Tris pH6.5, 17% polyethylene glycol 10000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 7, 2008
RadiationMonochromator: Cu Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 19393 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 42.56 Å2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 100

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Processing

Software
NameVersionClassification
APEXdata collection
CNSrefinement
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→35.419 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 978 5.15 %Random
Rwork0.1934 ---
all0.1953 ---
obs0.1953 18978 97.84 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.77 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4497 Å2-0 Å2-0 Å2
2--1.4497 Å20 Å2
3----2.8993 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 0 109 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053238
X-RAY DIFFRACTIONf_angle_d0.8564389
X-RAY DIFFRACTIONf_dihedral_angle_d16.3151178
X-RAY DIFFRACTIONf_chiral_restr0.061449
X-RAY DIFFRACTIONf_plane_restr0.003573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5997-2.73670.34481400.2859243494
2.7367-2.90810.29671510.2585248697
2.9081-3.13250.27931420.2134254997
3.1325-3.44750.27961410.2097256799
3.4475-3.94580.19741100.1882263399
3.9458-4.96910.17411640.14882619100
4.9691-35.42180.21061300.1829271299
Refinement TLS params.Method: refined / Origin x: 34.178 Å / Origin y: 46.1649 Å / Origin z: -0.6265 Å
111213212223313233
T0.2486 Å20.0333 Å2-0.0358 Å2-0.2266 Å20.0048 Å2--0.2238 Å2
L0.5069 °2-0.4667 °20.1628 °2-0.745 °2-0.0844 °2--0.3093 °2
S0.0649 Å °-0.0014 Å °-0.1001 Å °-0.0727 Å °-0.0322 Å °0.0737 Å °0.0848 Å °-0.0527 Å °-0 Å °
Refinement TLS groupSelection details: all

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