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- PDB-8v8q: HUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH MERS-COV EPITOPE ... -

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Basic information

Entry
Database: PDB / ID: 8v8q
TitleHUMAN LEUKOCYTE ANTIGEN B*07:02 IN COMPLEX WITH MERS-COV EPITOPE N95-103 (A95S 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


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 / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 ...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 / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / : / : / 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 / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / defense response / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 / recycling endosome membrane / 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 / Interferon alpha/beta signaling / MHC class II protein complex binding / 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 / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / early endosome membrane / host cell Golgi apparatus / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / ribonucleoprotein complex / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome
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
BICARBONATE ION / DI(HYDROXYETHYL)ETHER / Nucleoprotein / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 MERS-CoV EPITOPE N95-103 (A95S mutant)
Authors: Oltean, N. / Nyovanie, S. / Hashem, A. / Patskovska, L. / Patskovsky, Y. / Krogsgaard, M.
History
DepositionDec 5, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,6268
Polymers45,2563
Non-polymers3705
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.858, 153.872, 87.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

21C-105-

HOH

31C-111-

HOH

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 32093.211 Da / Num. of mol.: 1 / 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.: 1
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, 1 molecules C

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


Mass: 1283.410 Da / Num. of mol.: 1 / Fragment: residues 95-103 / Mutation: A95S / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome-related coronavirus
References: UniProt: K9N4V7

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Non-polymers , 4 types, 424 molecules

#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.6 Å3/Da / Density % sol: 52.69 % / Description: Thin plate
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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2023
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.85→29.19 Å / Num. obs: 40656 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Rrim(I) all: 0.101 / Χ2: 1 / Net I/σ(I): 11.9
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2482 / CC1/2: 0.847 / Rpim(I) all: 0.316 / Rrim(I) all: 0.846 / Χ2: 0.98 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0257refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LG0

7lg0


Resolution: 1.85→28.92 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.2 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20956 1217 3 %RANDOM
Rwork0.16969 ---
obs0.17088 39413 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å20 Å2
2---1.76 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 23 419 3618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133307
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172847
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6624489
X-RAY DIFFRACTIONr_angle_other_deg1.3781.5816606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3925386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.52921.29217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85915525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9051532
X-RAY DIFFRACTIONr_chiral_restr0.0710.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023782
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02778
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_it4.7363.0511544
X-RAY DIFFRACTIONr_mcbond_other4.7373.0511543
X-RAY DIFFRACTIONr_mcangle_it5.8494.5511927
X-RAY DIFFRACTIONr_mcangle_other5.8474.5511928
X-RAY DIFFRACTIONr_scbond_it7.3433.6231763
X-RAY DIFFRACTIONr_scbond_other7.3413.6231764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.2415.1522562
X-RAY DIFFRACTIONr_long_range_B_refined10.00335.7043840
X-RAY DIFFRACTIONr_long_range_B_other10.04435.1043736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 74 -
Rwork0.251 2885 -
obs--100 %

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