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- PDB-3ewp: complex of substrate ADP-ribose with IBV Nsp3 ADRP domain -

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Basic information

Entry
Database: PDB / ID: 3ewp
Titlecomplex of substrate ADP-ribose with IBV Nsp3 ADRP domain
ComponentsNon-structural protein 3
KeywordsHYDROLASE / Globular like / Cytoplasm / Membrane / Metal-binding / Protease / Ribosomal frameshifting / RNA-binding / Thiol protease / Transmembrane / Zinc / Zinc-finger
Function / homology
Function and homology information


viral genome replication / omega peptidase activity / transferase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy ...viral genome replication / omega peptidase activity / transferase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / proteolysis / RNA binding / zinc ion binding / membrane
Similarity search - Function
Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Coronavirus 3Ecto domain profile. / Papain-like viral protease, palm and finger domains, coronavirus / : ...Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Coronavirus 3Ecto domain profile. / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / Replicase polyprotein 1a
Similarity search - Component
Biological speciesAvian infectious bronchitis virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsXu, Y. / Cong, L. / Chen, C. / Wei, L. / Zhao, Q. / Xu, X. / Ma, Y. / Bartlam, M. / Rao, Z.
CitationJournal: J.Virol. / Year: 2009
Title: Crystal structures of two coronavirus ADP-ribose-1''-monophosphatases and their complexes with ADP-Ribose: a systematic structural analysis of the viral ADRP domain.
Authors: Xu, Y. / Cong, L. / Chen, C. / Wei, L. / Zhao, Q. / Xu, X. / Ma, Y. / Bartlam, M. / Rao, Z.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 3
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5274
Polymers38,4092
Non-polymers1,1192
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7642
Polymers19,2041
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7642
Polymers19,2041
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.364, 43.985, 49.266
Angle α, β, γ (deg.)78.25, 79.45, 73.39
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Non-structural protein 3 / nsp3 / Papain-like proteinase / PL-PRO / p195


Mass: 19204.291 Da / Num. of mol.: 2 / Fragment: Nsp3 ADRP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian infectious bronchitis virus / Gene: 1a / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P0C6V5, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 0.12M Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 22% w/v PEG 3350 , VAPOR DIFFUSION, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 12, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22223 / % possible obs: 82.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.299
Reflection shellResolution: 2→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.6 / Num. unique all: 68291 / % possible all: 85.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.249 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 1060 5.2 %RANDOM
Rwork0.17557 ---
obs0.17846 19345 93.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0.02 Å20.05 Å2
2---0.03 Å2-0.02 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2633 0 72 200 2905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222742
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.9913714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8825338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87124.495109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88815452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.196158
X-RAY DIFFRACTIONr_chiral_restr0.1570.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022004
X-RAY DIFFRACTIONr_nbd_refined0.2110.21398
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21872
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2179
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.215
X-RAY DIFFRACTIONr_mcbond_it1.0561.51742
X-RAY DIFFRACTIONr_mcangle_it1.61222714
X-RAY DIFFRACTIONr_scbond_it2.43331147
X-RAY DIFFRACTIONr_scangle_it3.5084.51000
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 58 -
Rwork0.202 1231 -
obs--80.26 %

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