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- PDB-6ss7: Human Leukocyte Antigen Class I A02 Carrying LLWAGPMAV -

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Basic information

Entry
Database: PDB / ID: 6ss7
TitleHuman Leukocyte Antigen Class I A02 Carrying LLWAGPMAV
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • LEU-LEU-TRP-ALA-GLY-PRO-MET-ALA-VAL
KeywordsIMMUNE SYSTEM / Yellow Fever / Altered Peptide Ligand / Human Major Histocompatibility Complex / X-ray 3D Structure Determination
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / flavivirin / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / T cell 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 / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / 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 iron ion transport / regulation of erythrocyte differentiation / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / positive regulation of T cell activation / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / positive regulation of protein binding / 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 / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / antibacterial humoral response / late endosome membrane / sensory perception of smell / viral capsid / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / double-stranded RNA binding / nucleoside-triphosphate phosphatase / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / amyloid fibril formation / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / intracellular iron ion homeostasis / learning or memory / RNA helicase activity / defense response to Gram-positive bacterium / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / immune response / RNA helicase
Similarity search - Function
Flavivirus non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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 non-structural protein NS2B / Flavivirus capsid protein C superfamily / 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, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 E-set / Immunoglobulin C-Type / Immunoglobulin C1-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 / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / Genome polyprotein / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Yellow fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsRizkallah, P.J. / Bovay, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_179570 Switzerland
CitationJournal: Mol.Immunol. / Year: 2020
Title: Identification of a superagonist variant of the immunodominant Yellow fever virus epitope NS4b214-222by combinatorial peptide library screening.
Authors: Bovay, A. / Zoete, V. / Rizkallah, P.J. / Beck, K. / Delbreil, P. / Speiser, D.E. / Cole, D.K. / Fuertes Marraco, S.A.
History
DepositionSep 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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, A-2 alpha chain
B: Beta-2-microglobulin
C: LEU-LEU-TRP-ALA-GLY-PRO-MET-ALA-VAL
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: LEU-LEU-TRP-ALA-GLY-PRO-MET-ALA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,66132
Polymers89,5766
Non-polymers2,08626
Water4,900272
1
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: LEU-LEU-TRP-ALA-GLY-PRO-MET-ALA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,59913
Polymers44,7883
Non-polymers81210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-95 kcal/mol
Surface area19310 Å2
MethodPISA
2
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: LEU-LEU-TRP-ALA-GLY-PRO-MET-ALA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,06219
Polymers44,7883
Non-polymers1,27416
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-72 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.560, 169.250, 49.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31951.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#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 (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide LEU-LEU-TRP-ALA-GLY-PRO-MET-ALA-VAL


Mass: 957.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Yellow fever virus / References: UniProt: P03314*PLUS

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Non-polymers , 5 types, 298 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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Cacodylate pH 6.0, 0.2 M Ammonium Sulphate, 25% PEG 4000. A2/LLW-7I crystals were grown in 0.1 M Mes pH 7.0, 0.2 M Ammonium Sulphate, 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.36→84.62 Å / Num. obs: 41105 / % possible obs: 99.6 % / Redundancy: 7.2 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.145 / Rrim(I) all: 0.288 / Net I/σ(I): 6.3
Reflection shellResolution: 2.36→2.42 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.713 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2956 / CC1/2: 0.484 / Rpim(I) all: 0.988 / Rrim(I) all: 1.982 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→84.62 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.861 / SU B: 15.316 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3044 1756 5.1 %RANDOM
Rwork0.2255 ---
obs0.2295 32915 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.31 Å2 / Biso mean: 35.344 Å2 / Biso min: 10.19 Å2
Baniso -1Baniso -2Baniso -3
1--28.96 Å2-0 Å2-0 Å2
2--40.55 Å20 Å2
3----11.59 Å2
Refinement stepCycle: final / Resolution: 2.5→84.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 122 272 6710
Biso mean--51.33 30.52 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196608
X-RAY DIFFRACTIONr_bond_other_d0.0020.025758
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.9348950
X-RAY DIFFRACTIONr_angle_other_deg1.077313342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2785766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01823.121346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.028151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9311556
X-RAY DIFFRACTIONr_chiral_restr0.1130.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217308
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021468
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 135 -
Rwork0.276 2388 -
all-2523 -
obs--99.14 %
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)
11.9168-0.26290.00183.1257-0.84571.5310.0169-0.0123-0.3070.07190.0405-0.15660.12980.1046-0.05740.0803-0.0284-0.01180.0423-0.0190.076444.528330.083814.7196
24.74951.48372.99381.42492.63395.09320.04640.3602-0.1796-0.140.0168-0.0601-0.05390.0662-0.06320.21180.03480.01370.0433-0.03980.160518.43249.55740.6443
34.74461.1432-2.10072.3449-0.80443.0221-0.0459-0.00620.05410.01530.15180.22330.1467-0.2301-0.10590.0885-0.0145-0.03360.03320.02210.036517.26527.9115.1956
41.72230.1898-0.01053.08111.13111.41550.0180.0430.31550.1236-0.00690.168-0.1398-0.0268-0.01110.0908-0.02760.02470.02110.00550.067616.901756.29338.9631
54.47221.0098-2.90162.1111-1.70594.88940.27520.41160.2629-0.126-0.05320.1777-0.1507-0.1702-0.22190.18010.0008-0.00820.06020.0120.131343.717776.064225.3771
64.6231.14871.75132.54191.33013.02920.0479-0.1590.0265-0.07450.0183-0.32-0.13490.3368-0.06630.1013-0.04520.0340.0806-0.00460.055444.07458.237139.8317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 180
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

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