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- PDB-6iex: Crystal structure of HLA-B*4001 in complex with SARS-CoV derived ... -

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Basic information

Entry
Database: PDB / ID: 6iex
TitleCrystal structure of HLA-B*4001 in complex with SARS-CoV derived peptide N216-225 GETALALLLL
Components
  • Beta-2-microglobulin
  • GLY-GLU-THR-ALA-LEU-ALA-LEU-LEU-LEU-LEU
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA-B*4001 / SARS-CoV / N216-225
Function / homology
Function and homology information


SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / Maturation of nucleoprotein / antigen processing and presentation / SARS-CoV-1 modulates host translation machinery / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry ...SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / Maturation of nucleoprotein / antigen processing and presentation / SARS-CoV-1 modulates host translation machinery / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / 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 epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / viral capsid / sensory perception of smell / SARS-CoV-1 activates/modulates innate immune responses / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / viral nucleocapsid / ER-Phagosome pathway / early endosome membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / amyloid fibril formation / molecular adaptor activity / protein homotetramerization / host cell Golgi apparatus / intracellular iron ion homeostasis / learning or memory / host cell perinuclear region of cytoplasm / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / ribonucleoprotein complex / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / DNA-templated transcription / DNA binding / : / RNA binding / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / MHC class I, alpha chain, C-terminal ...Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / MHC class I antigen / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
SARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.314 Å
AuthorsJi, W. / Niu, L. / Peng, W. / Zhang, Y. / Shi, Y. / Qi, J. / Gao, G.F. / Liu, W.J.
CitationJournal: Mol.Immunol. / Year: 2019
Title: Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner.
Authors: Ji, W. / Niu, L. / Peng, W. / Zhang, Y. / Cheng, H. / Gao, F. / Shi, Y. / Qi, J. / Gao, G.F. / Liu, W.J.
History
DepositionSep 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: GLY-GLU-THR-ALA-LEU-ALA-LEU-LEU-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)44,6873
Polymers44,6873
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-20 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.482, 69.274, 120.936
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen


Mass: 31794.154 Da / Num. of mol.: 1 / Fragment: UNP residues 25-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: F4NBU6, UniProt: A0A499S0B6*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P61769
#3: Protein/peptide GLY-GLU-THR-ALA-LEU-ALA-LEU-LEU-LEU-LEU


Mass: 1013.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SARS coronavirus / References: UniProt: P59595*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate tribasic dehydrate, pH 6.5 and 18% w-v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å
DetectorType: SDMS / Detector: FILM / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19343 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 20.3
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.314→41.832 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 0 / Phase error: 28.09
RfactorNum. reflection% reflection
Rfree0.2606 985 5.09 %
Rwork0.2108 --
obs0.2133 19343 97.21 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 30.166 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.5873 Å20 Å2-0 Å2
2--16.2802 Å20 Å2
3----0.6929 Å2
Refinement stepCycle: LAST / Resolution: 2.314→41.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 0 113 3255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063227
X-RAY DIFFRACTIONf_angle_d0.9174375
X-RAY DIFFRACTIONf_dihedral_angle_d17.8541203
X-RAY DIFFRACTIONf_chiral_restr0.067452
X-RAY DIFFRACTIONf_plane_restr0.003577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.314-2.4360.36491340.26242387X-RAY DIFFRACTION91
2.436-2.58860.30741280.2442544X-RAY DIFFRACTION96
2.5886-2.78840.3021310.24012589X-RAY DIFFRACTION97
2.7884-3.06890.35421580.23422626X-RAY DIFFRACTION99
3.0689-3.51280.24661440.21562655X-RAY DIFFRACTION99
3.5128-4.4250.23111340.1832721X-RAY DIFFRACTION100
4.425-41.83930.21421560.1982836X-RAY DIFFRACTION99
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)
10.68940.0469-0.36670.555-0.08120.4234-0.0150.0526-0.0764-0.02660.0538-0.09560.01560.182800.21760.0043-0.00910.22380.00180.197115.064610.33528.8548
20.53980.4305-0.1230.3539-0.17360.4530.17350.17620.1196-0.0555-0.00090.0413-0.1117-0.233800.28190.03440.02950.30380.08860.367-11.56391.976329.8119
30.1657-0.01590.03730.11280.19090.3491-0.05430.0118-0.0646-0.17970.05250.03790.0832-0.187-00.25080.02650.0050.27860.07730.24225.24962.806433.8358
40.16150.0598-0.01540.0880.02030.0815-0.08810.0207-0.0023-0.1725-0.0299-0.47560.07120.19430.00080.30780.0213-0.00380.38720.10580.449915.49216.814135.8255
50.13750.10570.04630.1058-0.00370.0621-0.00390.1796-0.1911-0.2116-0.03240.02450.1271-0.0020.00180.25240.02270.00780.2790.09190.346510.06446.166725.873
60.0165-0.0382-0.04440.08550.10.1165-0.0021-0.18210.02380.2499-0.00230.1145-0.05490.075600.4383-0.0256-0.04350.3760.06180.33529.96528.275142.1471
70.015-0.0132-0.02130.01160.01860.02930.0762-0.17120.00730.05360.02260.1727-0.1902-0.13200.32630.0168-0.01870.55080.00960.47232.16974.810642.1458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:174)
2X-RAY DIFFRACTION2chain 'A' and (resseq 175:274)
3X-RAY DIFFRACTION3chain 'B' and (resseq 1:28)
4X-RAY DIFFRACTION4chain 'B' and (resseq 29:51)
5X-RAY DIFFRACTION5chain 'B' and (resseq 52:71)
6X-RAY DIFFRACTION6chain 'B' and (resseq 72:90)
7X-RAY DIFFRACTION7chain 'B' and (resseq 91:99)

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