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- PDB-3ejf: Crystal structure of IBV X-domain at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 3ejf
TitleCrystal structure of IBV X-domain at pH 8.5
ComponentsNon-structural protein 3
KeywordsHYDROLASE / IBV / coronavirus / X-domain / macro domain / Nsp3 / ADRP / Ribosomal frameshifting / RNA-binding
Function / homology
Function and homology information


Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / 5'-3' DNA helicase activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / endonuclease activity ...Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / 5'-3' DNA helicase activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / 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
Nonstructural protein 14, gammacoronavirus / Nonstructural protein 15, middle domain, gammacoronavirus / Nonstructural protein 15, N-terminal, gammacoronavirus / RNA-dependent RNA polymerase, gammacoronavirus / 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 ...Nonstructural protein 14, gammacoronavirus / Nonstructural protein 15, middle domain, gammacoronavirus / Nonstructural protein 15, N-terminal, gammacoronavirus / RNA-dependent RNA polymerase, gammacoronavirus / 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 / Viral (Superfamily 1) RNA helicase / 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. / 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 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / : / Papain-like viral protease, palm and finger domains, coronavirus / Coronavirus 3Ecto domain profile. / : / 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
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesAvian infectious bronchitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPiotrowski, Y. / Hansen, G. / Hilgenfeld, R.
CitationJournal: Protein Sci. / Year: 2009
Title: Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property.
Authors: Piotrowski, Y. / Hansen, G. / Boomaars-van der Zanden, A.L. / Snijder, E.J. / Gorbalenya, A.E. / Hilgenfeld, R.
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)19,4201
Polymers19,4201
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.207, 79.811, 99.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

21A-364-

HOH

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Components

#1: Protein Non-structural protein 3 / nsp3, Papain-like proteinase, PL-PRO, p195 / nsp3 / PP1AB / ORF1AB Polyprotein


Mass: 19420.438 Da / Num. of mol.: 1 / Fragment: Macro domain, UNP residues 1005-1176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian infectious bronchitis virus (strain Beaudette)
Gene: 1a / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P0C6Y1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 285.15 K / pH: 8.5
Details: 30% PEG 4000, 0.1 M TRIS PH 8.5, 0.2 M MAGENSIUM CHLORIDE, temperature 285.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8081
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8081 Å / Relative weight: 1
ReflectionResolution: 1.6→24.82 Å / Num. obs: 22201 / % possible obs: 97.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 18.371
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.244 / % possible all: 97.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.3.0037refinement
PDB_EXTRACT3.006data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→24.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.37 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1136 5.1 %RANDOM
Rwork0.169 ---
obs0.171 22172 97.7 %-
all-21036 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 0 212 1537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221359
X-RAY DIFFRACTIONr_bond_other_d0.0010.02898
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9491848
X-RAY DIFFRACTIONr_angle_other_deg0.88432212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1375177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52924.83962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.611154
X-RAY DIFFRACTIONr_chiral_restr0.0820.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021525
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
X-RAY DIFFRACTIONr_nbd_refined0.2120.2287
X-RAY DIFFRACTIONr_nbd_other0.1820.2886
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2685
X-RAY DIFFRACTIONr_nbtor_other0.0870.2683
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2135
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0991.51098
X-RAY DIFFRACTIONr_mcbond_other0.2091.5344
X-RAY DIFFRACTIONr_mcangle_it1.2321367
X-RAY DIFFRACTIONr_scbond_it2.1163603
X-RAY DIFFRACTIONr_scangle_it2.8814.5475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 85 -
Rwork0.188 1481 -
obs--94.62 %

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