[English] 日本語
Yorodumi
- PDB-5ylx: Integrated illustration of a valid epitope based on the SLA class... -

+
Open data


ID or keywords:

Loading...

-
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-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 / symbiont-mediated suppression of host PKR/eIFalpha signaling / Neutrophil degranulation / host cell endoplasmic reticulum / 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 / symbiont-mediated suppression of host PKR/eIFalpha signaling / Neutrophil degranulation / host cell endoplasmic reticulum / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / host cell membrane / RNA nuclease activity / protein serine/threonine kinase inhibitor activity / antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / DNA helicase activity / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / Lyases; Phosphorus-oxygen lyases / endonuclease activity / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / RNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lyase activity / immune response / viral protein processing / host cell perinuclear region of cytoplasm / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / signaling receptor binding / serine-type endopeptidase activity / external side of plasma membrane / viral translational frameshifting / lysosomal membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / ATP hydrolysis activity / proteolysis / extracellular space / RNA binding / extracellular region / zinc ion binding / ATP binding
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, 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 / Nsp1alpha N-terminal zinc finger / Nonstructural protein 10, zinc-binding domain, arterivirus / NSP11, NendoU domain, arterivirus / NSP11, N-terminal, arterivirus / PRRSV nonstructural protein 11 N-terminal domain / 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 core domain / 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 / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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. / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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. / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / 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 / Replicase polyprotein 1ab / 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
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more