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- PDB-5ylx: Integrated illustration of a valid epitope based on the SLA class... -

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Basic information

Entry
Database: PDB / ID: 5ylx
TitleIntegrated illustration of a valid epitope based on the SLA class I structure and tetramer technique could carry forward the development of molecular vaccine in swine species
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
  • PRRSV-NSP9-TMP9 peptide
KeywordsIMMUNE SYSTEM / MHC / CTL response / tetramer
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / : / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / : / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / Lyases; Phosphorus-oxygen lyases / late endosome membrane / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / immune response / RNA-directed RNA polymerase / lysosomal membrane / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / extracellular region / ATP binding / membrane
Similarity search - Function
Nonstructural protein 10, 1B domain, arterivirus / Replicase polyprotein 1ab, peptidase C33-associated domain / Peptidase_C33-associated domain / Arterivirus polyprotein, nsp2, immunogenic region / Arterivirus papain-like cysteine protease beta (PCPbeta) domain superfamily / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain superfamily / Porcine arterivirus-type cysteine proteinase alpha / Equine arteritis virus putative proteinase / Immunogenic region of nsp2 protein of arterivirus polyprotein / Nonstructural protein 10, zinc-binding domain, arterivirus ...Nonstructural protein 10, 1B domain, arterivirus / Replicase polyprotein 1ab, peptidase C33-associated domain / Peptidase_C33-associated domain / Arterivirus polyprotein, nsp2, immunogenic region / Arterivirus papain-like cysteine protease beta (PCPbeta) domain superfamily / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain superfamily / Porcine arterivirus-type cysteine proteinase alpha / Equine arteritis virus putative proteinase / Immunogenic region of nsp2 protein of arterivirus polyprotein / Nonstructural protein 10, zinc-binding domain, arterivirus / NSP11, NendoU domain, arterivirus / NSP11, N-terminal, arterivirus / Arteriviridae zinc-binding (AV ZBD) domain profile. / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain / Arterivirus Nsp2, peptidase C33 / Equine arteritis virus peptidase S32 / Serine protease, chymotrypsin-like serine protease, C-terminal / Arterivirus NSP4 peptidase domain / Arterivirus papain-like cysteine protease beta (PCPbeta) domain / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp7 alpha superfamily / Equine arterivirus Nsp2-type cysteine proteinase / Equine arteritis virus serine endopeptidase S32 / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp4 proteinase domain profile. / Arterivirus nsp2 cysteine protease (AV CP) domain profile. / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain profile. / Arterivirus papain-like cysteine protease beta (PCPbeta) domain profile. / Viral (Superfamily 1) RNA helicase / 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 / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / ORF1ab polyprotein / Beta-2-microglobulin / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSus scrofa (pig)
Porcine reproductive and respiratory syndrome virus
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsPan, X.C. / Wei, X.H. / Zhang, N. / Xia, C.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31201887 China
863 Project of the China Ministry of Science and Technology2013AA102503 China
973 Project of the China Ministry of Science and Technology2013CB835302 China
CitationJournal: Front Immunol / Year: 2019
Title: Illumination of PRRSV Cytotoxic T Lymphocyte Epitopes by the Three-Dimensional Structure and Peptidome of Swine Lymphocyte Antigen Class I (SLA-I).
Authors: Pan, X. / Zhang, N. / Wei, X. / Jiang, Y. / Chen, R. / Li, Q. / Liang, R. / Zhang, L. / Ma, L. / Xia, C.
History
DepositionOct 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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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: PRRSV-NSP9-TMP9 peptide


Theoretical massNumber of molelcules
Total (without water)43,8863
Polymers43,8863
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-22 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.058, 74.059, 98.596
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: 31399.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SLA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: H6TIB1
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / Lactollin


Mass: 11431.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q07717
#3: Protein/peptide PRRSV-NSP9-TMP9 peptide


Mass: 1054.215 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Porcine reproductive and respiratory syndrome virus
References: UniProt: I6YDJ5, UniProt: Q9YN02*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Ammonium acetate, 0.1M BIS-TRIS pH5.5, 17% PEG 10000, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 24678 / % possible obs: 99.5 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 27.366
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 7.517 / Rsym value: 0.286 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX(phenix.refine: 1.5_2)refinement
RefinementResolution: 2.2→29.607 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 0.14 / Phase error: 21.63
RfactorNum. reflection% reflection
Rfree0.2432 1265 5.13 %
Rwork0.2001 --
obs0.2023 24678 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 40.016 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9444 Å20 Å2-0 Å2
2--1.0093 Å20 Å2
3----2.9537 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3092 0 0 343 3435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143181
X-RAY DIFFRACTIONf_angle_d1.144317
X-RAY DIFFRACTIONf_dihedral_angle_d19.4461162
X-RAY DIFFRACTIONf_chiral_restr0.094441
X-RAY DIFFRACTIONf_plane_restr0.005572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1987-2.28670.26091340.2012471X-RAY DIFFRACTION95
2.2867-2.39070.26531440.20952482X-RAY DIFFRACTION96
2.3907-2.51670.26271380.20182546X-RAY DIFFRACTION97
2.5167-2.67430.28751300.20812563X-RAY DIFFRACTION97
2.6743-2.88060.26711390.20742590X-RAY DIFFRACTION98
2.8806-3.17020.25281460.20242618X-RAY DIFFRACTION99
3.1702-3.62820.21841470.19342646X-RAY DIFFRACTION100
3.6282-4.56840.20111600.1672674X-RAY DIFFRACTION100
4.5684-29.61010.22191270.19612823X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -7.1259 Å / Origin y: 25.8216 Å / Origin z: 15.7159 Å
111213212223313233
T0.0637 Å20.0069 Å2-0.001 Å2-0.0606 Å2-0.0069 Å2--0.0597 Å2
L0.382 °20.2316 °20.1275 °2-0.3257 °20.0865 °2--0.0687 °2
S0.0179 Å °0.02 Å °0.0153 Å °0.0341 Å °-0.0002 Å °0.0013 Å °-0.0066 Å °-0.0115 Å °0 Å °
Refinement TLS groupSelection details: all

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