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- PDB-1yo4: Solution Structure of the SARS Coronavirus ORF 7a coded X4 protein -

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Basic information

Entry
Database: PDB / ID: 1yo4
TitleSolution Structure of the SARS Coronavirus ORF 7a coded X4 protein
ComponentsHypothetical protein X4
KeywordsVIRAL PROTEIN / beta-sandwich / immunoglobulin-like domain
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / SARS-CoV-1-mediated effects on programmed cell death / Virion Assembly and Release / host cell endoplasmic reticulum / host cell Golgi membrane / Attachment and Entry / symbiont-mediated activation of host apoptosis / SARS-CoV-1 activates/modulates innate immune responses / host cell Golgi apparatus / suppression by virus of host tetherin activity ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / SARS-CoV-1-mediated effects on programmed cell death / Virion Assembly and Release / host cell endoplasmic reticulum / host cell Golgi membrane / Attachment and Entry / symbiont-mediated activation of host apoptosis / SARS-CoV-1 activates/modulates innate immune responses / host cell Golgi apparatus / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / virion membrane / plasma membrane
Similarity search - Function
SARS coronavirus X4 / Structural accessory protein ORF7a, SARS-CoV-like / ORF7a superfamily, coronavirus / Structural accessory protein ORF7a, SARS-CoV-like, X4e domain / Betacoronavirus NS7A protein / X4e domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSARS coronavirus
MethodSOLUTION NMR / molecular dynamics simulated annealing
AuthorsHaenel, K. / Stangler, T. / Stoldt, M. / Willbold, D.
CitationJournal: J.Biomed.Sci. / Year: 2006
Title: Solution structure of the X4 protein coded by the SARS related coronavirus reveals an immunoglobulin like fold and suggests a binding activity to integrin I domains.
Authors: Haenel, K. / Stangler, T. / Stoldt, M. / Willbold, D.
History
DepositionJan 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein X4


Theoretical massNumber of molelcules
Total (without water)9,9091
Polymers9,9091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #8closest to the average

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Components

#1: Protein Hypothetical protein X4 / ORF7a Protein / ORF8


Mass: 9909.089 Da / Num. of mol.: 1 / Fragment: N-terminal ectodomain(residues 1-84)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P59635

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.4mM ORF7a Protein U-15N,13C; 1mM Sodium Acetate (deuterated), 93% H2O, 7% D2O
Solvent system: 93% H2O/7% D2O
Sample conditionsIonic strength: 1mM sodium acetate / pH: 5 / Pressure: ambient / Temperature: 315 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Dn.a.collection
NMRPipen.a.Delaglio, F.processing
CARA1.1.5Keller, R.data analysis
ARIA1.2Nilges, M.structure solution
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: molecular dynamics simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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