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- PDB-8utc: HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE... -

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Basic information

Entry
Database: PDB / ID: 8utc
TitleHUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B alpha chain
  • Nucleoprotein
KeywordsIMMUNE SYSTEM / Viral Protein / Complex
Function / homology
Function and homology information


response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle ...response to host immune response / viral RNA genome packaging / negative regulation of interferon-beta production / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / TAP binding / protection from natural killer cell mediated cytotoxicity / CD28 dependent PI3K/Akt signaling / 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 / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / : / : / secretory granule membrane / 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 / VEGFR2 mediated vascular permeability / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / molecular condensate scaffold activity / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / defense response / response to molecule of bacterial origin / HFE-transferrin receptor complex / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / DDX58/IFIH1-mediated induction of interferon-alpha/beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / RNA stem-loop binding / recycling endosome membrane / Interleukin-1 signaling / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / Interferon alpha/beta signaling / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / viral capsid / tertiary granule lumen / DAP12 signaling / PIP3 activates AKT signaling / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / protein refolding / viral nucleocapsid / early endosome membrane / host cell Golgi apparatus / protein homotetramerization / adaptive immune response / Translation of Structural Proteins / Virion Assembly and Release / amyloid fibril formation / host extracellular space / Induction of Cell-Cell Fusion
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 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
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / HLA class I histocompatibility antigen, B alpha chain / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOltean, N. / Nyovanie, S. / Hashem, A. / Patskovska, L. / Patskovsky, Y. / Krogsgaard, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1-TR001445-06-A1-S1 United States
CitationJournal: To Be Published
Title: HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH SARS-COV2 EPITOPE N105-113 (Y111F mutant)
Authors: Oltean, N. / Nyovanie, S. / Hashem, A. / Patskovska, L. / Patskovsky, Y. / Krogsgaard, M.
History
DepositionOct 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
E: Nucleoprotein
F: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,14912
Polymers90,5046
Non-polymers6456
Water5,170287
1
A: HLA class I histocompatibility antigen, B alpha chain
B: Beta-2-microglobulin
E: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7038
Polymers45,2523
Non-polymers4515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-42 kcal/mol
Surface area19060 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
F: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4464
Polymers45,2523
Non-polymers1941
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-14 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.067, 84.737, 154.189
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein HLA class I histocompatibility antigen, B alpha chain


Mass: 32093.211 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01889
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Nucleoprotein / N / Nucleocapsid protein / NC / Protein N


Mass: 1279.464 Da / Num. of mol.: 2 / Fragment: residues 105-113 (Uniprot numbering) / Mutation: Y7F / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9

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Non-polymers , 4 types, 293 molecules

#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.54 Å3/Da / Density % sol: 51.64 % / Description: tetragonal bipyramid
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES-NaOH, pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 2, 2023 / Details: SI 111 Crystal
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→44.23 Å / Num. obs: 36717 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 38.241 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.05 / Rrim(I) all: 0.132 / Χ2: 0.952 / Net I/σ(I): 10.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.042 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1816 / CC1/2: 0.692 / CC star: 0.904 / Rpim(I) all: 0.472 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data scaling
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0257refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7LG0

7lg0


Resolution: 2.4→44.23 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 18.074 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.384 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24027 1114 3 %RANDOM
Rwork0.18337 ---
obs0.18509 35556 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--1.6 Å2-0 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6309 0 39 287 6635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136548
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175635
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.6618891
X-RAY DIFFRACTIONr_angle_other_deg1.3091.57913053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.15766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.45921.088432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.833151021
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1971566
X-RAY DIFFRACTIONr_chiral_restr0.0710.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027497
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021561
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.5182.8783073
X-RAY DIFFRACTIONr_mcbond_other6.5172.8783072
X-RAY DIFFRACTIONr_mcangle_it8.0184.3143833
X-RAY DIFFRACTIONr_mcangle_other8.0174.3143834
X-RAY DIFFRACTIONr_scbond_it8.2423.3063475
X-RAY DIFFRACTIONr_scbond_other8.2423.3063475
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.0374.7315057
X-RAY DIFFRACTIONr_long_range_B_refined11.266337239
X-RAY DIFFRACTIONr_long_range_B_other11.28232.8117194
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A8482
12C8482
21B2946
22D2946
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 87 -
Rwork0.285 2569 -
obs--100 %
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)
11.5890.2066-1.61131.4308-0.30473.22240.0327-0.01470.0929-0.098-0.0082-0.0953-0.12080.0278-0.02450.06020.0358-0.03010.0437-0.03350.0461-17.1378-16.535512.6597
25.2141-0.1354-2.14291.29530.89332.6505-0.07060.0589-0.3907-0.1449-0.0663-0.06110.0959-0.06290.13690.07030.00940.01160.0051-0.00120.0344-16.9617-31.4568-0.4171
31.6226-0.4844-2.06780.50741.06963.47590.0619-0.0180.1515-0.0034-0.02930.1419-0.2013-0.0528-0.03250.26630.04420.0210.16710.01110.1382-19.6025-58.7635-15.0522
44.0374-1.0069-1.80015.2985-0.56023.9961-0.0263-0.014-0.64620.3293-0.01770.8180.0264-0.05650.0440.22770.08480.00970.1192-0.01320.1986-20.1897-73.446-2.2819
58.6064-0.117-0.9791.26211.10471.0592-0.1096-0.0005-0.15530.08760.05420.04730.07650.06950.05540.1779-0.0066-0.03630.17320.03070.0658-18.2856-19.560232.3223
68.43222.13331.5551.3618-0.68951.7263-0.10130.07011.32010.1573-0.11670.3345-0.30320.13460.2180.24320.10690.03510.14330.04240.2184-15.2905-61.6656-34.1946
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 301
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C1 - 301
4X-RAY DIFFRACTION4D0 - 99
5X-RAY DIFFRACTION5E1 - 101
6X-RAY DIFFRACTION6F1 - 9

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