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- PDB-3ew5: Structure of the tetragonal crystal form of X (ADRP) domain from FCoV -

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Basic information

Entry
Database: PDB / ID: 3ew5
TitleStructure of the tetragonal crystal form of X (ADRP) domain from FCoV
Componentsmacro domain of Non-structural protein 3
KeywordsRNA BINDING PROTEIN / coronavirus / macro / ADRP / X domain
Function / homology
Function and homology information


host cell membrane / viral genome replication / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 ...host cell membrane / viral genome replication / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / : / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain ...Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / : / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Coronavirus 3Ecto domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / 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
Similarity search - Domain/homology
SN-GLYCEROL-1-PHOSPHATE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesFeline infectious peritonitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWojdyla, J.A. / Manolaridis, I. / Tucker, P.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the X (ADRP) domain of nsp3 from feline coronavirus
Authors: Wojdyla, J.A. / Manolaridis, I. / Snijder, E.J. / Gorbalenya, A.E. / Coutard, B. / Piotrowski, Y. / Hilgenfeld, R. / Tucker, P.A.
History
DepositionOct 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: macro domain of Non-structural protein 3
B: macro domain of Non-structural protein 3
C: macro domain of Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,55216
Polymers55,3183
Non-polymers1,23413
Water1,42379
1
A: macro domain of Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8395
Polymers18,4391
Non-polymers4004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: macro domain of Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7785
Polymers18,4391
Non-polymers3394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: macro domain of Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9356
Polymers18,4391
Non-polymers4965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.130, 161.130, 98.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA36 - 6736 - 67
21BB36 - 6736 - 67
31CC36 - 6736 - 67
12AA77 - 7877 - 78
22BB77 - 7877 - 78
32CC77 - 7877 - 78
13AA82 - 9782 - 97
23BB82 - 9782 - 97
33CC82 - 9782 - 97
14AA104 - 162104 - 162
24BB104 - 162104 - 162
34CC104 - 162104 - 162
15AA166 - 183166 - 183
25BB166 - 183166 - 183
35CC166 - 183166 - 183
16AA501 - 502501 - 502
26BB501 - 502501 - 502
36CC501 - 502501 - 502

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Components

#1: Protein macro domain of Non-structural protein 3 / X (ADRP) domain


Mass: 18439.305 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline infectious peritonitis virus / Strain: FIPV WSU-79/1146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q98VG9
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H9O6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 5.766374 Å3/Da / Density % sol: 78.669434 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2008
RadiationMonochromator: Si(311) and Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 26271 / Num. obs: 26025 / % possible obs: 99.1 % / Observed criterion σ(I): -3
Reflection shellResolution: 3.01→3.19 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.4.0069refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→24.66 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 14.219 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.498 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24203 1225 5.1 %RANDOM
Rwork0.20014 ---
obs0.20228 22625 99.52 %-
all-22625 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.261 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.1→24.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3887 0 64 79 4030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224000
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9935413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94724.583168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.02715703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5271521
X-RAY DIFFRACTIONr_chiral_restr0.10.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212910
X-RAY DIFFRACTIONr_mcbond_it0.5411.52483
X-RAY DIFFRACTIONr_mcangle_it1.05424006
X-RAY DIFFRACTIONr_scbond_it1.32331517
X-RAY DIFFRACTIONr_scangle_it2.3814.51406
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A508tight positional0.240.05
B508tight positional0.320.05
C508tight positional0.210.05
A481medium positional1.530.5
B481medium positional2.90.5
C481medium positional1.490.5
A508tight thermal0.730.5
B508tight thermal0.70.5
C508tight thermal1.060.5
A481medium thermal0.782
B481medium thermal0.842
C481medium thermal1.062
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 94 -
Rwork0.34 1614 -
obs--99.94 %

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