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- PDB-9sl0: Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAV -

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Basic information

Entry
Database: PDB / ID: 9sl0
TitleCrystal structure of HLA-A0201 in complex with peptide LLWNGPMAV
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • NS5
KeywordsIMMUNE SYSTEM / HLA class I / Human leukocyte antigen class I / MHC class I / Major histocompatibility complex class I
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity ...antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / Interferon gamma signaling / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / ribonucleoside triphosphate phosphatase activity / viral capsid / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / double-stranded RNA binding / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / methyltransferase cap1 activity / learning or memory / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / symbiont-mediated activation of host autophagy / external side of plasma membrane / serine-type endopeptidase activity / lysosomal membrane / focal adhesion / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / virion attachment to host cell / GTP binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / proteolysis / extracellular space / extracellular exosome / extracellular region / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / 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. / helicase superfamily c-terminal domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin E-set / Immunoglobulin C1-set domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Yellow fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, Y. / Gfeller, D. / Guillaume, P. / Larabi, A. / Lau, K. / Pojer, F.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation320030-231333 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAV
Authors: Liu, Y. / Croce, G. / Tadros, D. / Moreno, D. / Michel, A. / Thierry, A-T / Genolet, R. / Perez, M. / Lani, R. / Guillaume, P. / Schmidt, J. / Teleman, M. / Lau, K. / Larabi, A. / Racle, J. ...Authors: Liu, Y. / Croce, G. / Tadros, D. / Moreno, D. / Michel, A. / Thierry, A-T / Genolet, R. / Perez, M. / Lani, R. / Guillaume, P. / Schmidt, J. / Teleman, M. / Lau, K. / Larabi, A. / Racle, J. / Speiser, D.E. / Pojer, F. / Dunn, S. / Baumgaertner, P. / Zoete, V. / Harari, A. / Gfeller, D.
History
DepositionSep 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / Item: _citation.title

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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: NS5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,17711
Polymers44,8653
Non-polymers3128
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.181, 80.201, 111.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31985.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Variant: HLA-A*02:01 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5I8L1
#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 / Variant: HLA-A*02:01 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide NS5


Mass: 1000.214 Da / Num. of mol.: 1 / Fragment: UNP residues 2470-2478 / Source method: obtained synthetically / Source: (synth.) Yellow fever virus / References: UniProt: W8FN10

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Non-polymers , 4 types, 208 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.005 M Cadmium chloride hemi(pentahydrate), 0.1 M Tris 8.5, 20% w/v PEG 4000 Clear-Strategy-Screen-II H3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS4 X 4M / Detector: PIXEL / Date: Nov 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.596→19.744 Å / Num. obs: 72436 / % possible obs: 99.64 % / Redundancy: 13.6 % / Biso Wilson estimate: 20.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.085 / Net I/σ(I): 18.6
Reflection shellResolution: 1.596→1.623 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3522 / CC1/2: 0.752

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Processing

Software
NameVersionClassification
PHENIX1.21.2-5419refinement
PHENIX1.21.2-5419phasing
autoPROCautoPROC 1.0.5 ()data processing
XDSJun 30, 2024 (BUILT 20241002data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.74 Å / SU ML: 0.2087 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9687
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2638 3731 5.17 %
Rwork0.2339 68462 -
obs0.2354 72193 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.74 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 14 200 3351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00593285
X-RAY DIFFRACTIONf_angle_d0.78424463
X-RAY DIFFRACTIONf_chiral_restr0.0517452
X-RAY DIFFRACTIONf_plane_restr0.0068586
X-RAY DIFFRACTIONf_dihedral_angle_d15.46681204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.32811010.29452421X-RAY DIFFRACTION94.85
1.62-1.640.29981330.28042489X-RAY DIFFRACTION99.58
1.64-1.660.32981260.27062502X-RAY DIFFRACTION99.62
1.66-1.680.29421390.27142500X-RAY DIFFRACTION99.81
1.68-1.710.32211560.26822490X-RAY DIFFRACTION99.7
1.71-1.740.35311360.28882515X-RAY DIFFRACTION99.74
1.74-1.760.30871450.27112529X-RAY DIFFRACTION99.85
1.76-1.790.2761390.26422488X-RAY DIFFRACTION99.77
1.79-1.830.35831470.27692545X-RAY DIFFRACTION99.85
1.83-1.860.34131210.26822505X-RAY DIFFRACTION99.81
1.86-1.90.27251290.2612519X-RAY DIFFRACTION99.59
1.9-1.940.291550.25122495X-RAY DIFFRACTION99.59
1.94-1.990.29451190.24892514X-RAY DIFFRACTION99.73
1.99-2.040.26481350.2552519X-RAY DIFFRACTION99.7
2.04-2.090.29851400.24652536X-RAY DIFFRACTION99.66
2.09-2.150.25051470.2372518X-RAY DIFFRACTION99.63
2.15-2.220.27581500.23312543X-RAY DIFFRACTION100
2.22-2.30.2671440.23322514X-RAY DIFFRACTION99.96
2.3-2.390.23731500.23582527X-RAY DIFFRACTION99.93
2.39-2.50.27021360.24282569X-RAY DIFFRACTION99.93
2.5-2.630.25971290.24242562X-RAY DIFFRACTION99.96
2.63-2.80.25851280.23482552X-RAY DIFFRACTION99.96
2.8-3.010.25241500.22812570X-RAY DIFFRACTION100
3.01-3.310.25231510.22732561X-RAY DIFFRACTION99.93
3.31-3.790.24061560.21082586X-RAY DIFFRACTION100
3.79-4.770.23411400.18362624X-RAY DIFFRACTION100
4.77-19.740.25591290.24512769X-RAY DIFFRACTION100

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