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- PDB-1xak: STRUCTURE OF THE SARS-CORONAVIRUS ORF7A ACCESSORY PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1xak
TitleSTRUCTURE OF THE SARS-CORONAVIRUS ORF7A ACCESSORY PROTEIN
ComponentsSARS ORF7A ACCESSORY PROTEIN
KeywordsVIRAL PROTEIN / I-SET IG DOMAIN / BETA SANDWICH / Structural Genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / Virion Assembly and Release / SARS-CoV-1-mediated effects on programmed cell death / host cell endoplasmic reticulum / host cell Golgi membrane / Attachment and Entry / : / 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 / Virion Assembly and Release / SARS-CoV-1-mediated effects on programmed cell death / host cell endoplasmic reticulum / host cell Golgi membrane / Attachment and Entry / : / 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 type I interferon-mediated signaling pathway / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsNelson, C.A. / Lee, C.A. / Fremont, D.H. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Structure / Year: 2005
Title: Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein.
Authors: Nelson, C.A. / Pekosz, A. / Lee, C.A. / Diamond, M.S. / Fremont, D.H.
History
DepositionAug 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: SARS ORF7A ACCESSORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,4251
Polymers9,4251
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.100, 37.100, 55.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein SARS ORF7A ACCESSORY PROTEIN


Mass: 9424.540 Da / Num. of mol.: 1 / Fragment: N-TERMINAL ECTODOMAIN (residues 14-96)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Plasmid: pET-21a (EMD Biosciences) / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3)RIL codon (+) E.coli cells (Stratagene)
References: UniProt: P59635
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.35
Details: 16% PEG 400, 100 mM sodium acetate, pH 5.35, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 7744 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.047 / Net I/σ(I): 34.9
Reflection shellResolution: 1.8→1.88 Å / Mean I/σ(I) obs: 5.2 / Rsym value: 0.297 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→18.55 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 768789.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 422 5.5 %RANDOM
Rwork0.223 ---
obs0.223 7741 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 93.0056 Å2 / ksol: 0.375932 e/Å3
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å22.38 Å20 Å2
2--1.61 Å20 Å2
3----3.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.8→18.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms533 0 0 142 675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 78 6.1 %
Rwork0.291 1198 -
obs-984 97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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