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- PDB-8wqq: Proteomics study reveals that ASFV g5Rp protein interacts with eu... -

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Basic information

Entry
Database: PDB / ID: 8wqq
TitleProteomics study reveals that ASFV g5Rp protein interacts with eukaryotic translation initiation factor 5A and may regulate host translation
ComponentsmRNA-decapping protein g5R
KeywordsVIRAL PROTEIN / African swine fever virus / g5Rp / quantitative proteomics / EIF5A / protein-protein interaction / VIRUS
Function / homology
Function and homology information


AMP biosynthetic process / diphosphoinositol-polyphosphate diphosphatase activity / diphosphoinositol-polyphosphate diphosphatase / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / host cell rough endoplasmic reticulum / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / ATP biosynthetic process / symbiont-mediated suppression of host gene expression / RNA binding / metal ion binding
Similarity search - Function
: / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
mRNA-decapping protein g5R
Similarity search - Component
Biological speciesASFV-like virus WU
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLiang, R.Y. / Xu, C.M. / Zhao, X.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32302912 China
CitationJournal: To Be Published
Title: Proteomics study reveals that ASFV g5Rp protein interacts with eukaryotic translation initiation factor 5A and may regulate host translation.
Authors: Liang, R.Y. / Xu, C.M.
History
DepositionOct 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA-decapping protein g5R
B: mRNA-decapping protein g5R


Theoretical massNumber of molelcules
Total (without water)58,1972
Polymers58,1972
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-9 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.199, 77.296, 96.779
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 mRNA-decapping protein g5R


Mass: 29098.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASFV-like virus WU / Gene: Ba71V-102 / Production host: Escherichia coli (E. coli) / References: UniProt: P32092
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES Sodium, pH 7.5,1.5M Lithium Sulfate monophydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.3→30.198 Å / Num. obs: 25174 / % possible obs: 99.31 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 15.4
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.778 / Num. unique obs: 1627

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30.198 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 28.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2873 1978 7.86 %
Rwork0.2375 --
obs0.2415 25174 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→30.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4092 0 0 191 4283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064192
X-RAY DIFFRACTIONf_angle_d0.9475644
X-RAY DIFFRACTIONf_dihedral_angle_d8.272534
X-RAY DIFFRACTIONf_chiral_restr0.052594
X-RAY DIFFRACTIONf_plane_restr0.006710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.35750.31241350.26571627X-RAY DIFFRACTION99
2.3575-2.42120.32831500.25411630X-RAY DIFFRACTION100
2.4212-2.49240.2861380.25411660X-RAY DIFFRACTION100
2.4924-2.57280.32161370.261632X-RAY DIFFRACTION100
2.5728-2.66470.32971380.26761646X-RAY DIFFRACTION100
2.6647-2.77140.32751430.25561658X-RAY DIFFRACTION100
2.7714-2.89740.29581380.26081646X-RAY DIFFRACTION100
2.8974-3.050.30531450.26361642X-RAY DIFFRACTION100
3.05-3.24090.29731440.25691666X-RAY DIFFRACTION100
3.2409-3.49080.31711370.25241660X-RAY DIFFRACTION100
3.4908-3.84150.37741360.26551567X-RAY DIFFRACTION94
3.8415-4.39590.23331440.2081665X-RAY DIFFRACTION98
4.3959-5.53280.25661440.19751717X-RAY DIFFRACTION100

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