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- PDB-3jzt: Structure of a cubic crystal form of X (ADRP) domain from FCoV wi... -

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Entry
Database: PDB / ID: 3jzt
TitleStructure of a cubic crystal form of X (ADRP) domain from FCoV with ADP-ribose
Componentsmacro domain of Non-structural protein 3
KeywordsRNA BINDING PROTEIN / ADRP domain / X domain / macro domain / ADP-ribose / coronavirus
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
ADENOSINE-5-DIPHOSPHORIBOSE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesFeline coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.91 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
DepositionSep 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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
D: macro domain of Non-structural protein 3
E: macro domain of Non-structural protein 3
F: macro domain of Non-structural protein 3
G: macro domain of Non-structural protein 3
H: macro domain of Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,28614
Polymers147,5148
Non-polymers1,7726
Water0
1
A: macro domain of Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4752
Polymers18,4391
Non-polymers351
Water0
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)19,0223
Polymers18,4391
Non-polymers5822
Water0
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)18,9992
Polymers18,4391
Non-polymers5591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: macro domain of Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,4391
Non-polymers5591
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4391
Polymers18,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4391
Polymers18,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: macro domain of Non-structural protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4752
Polymers18,4391
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: macro domain of Non-structural protein 3


Theoretical massNumber of molelcules
Total (without water)18,4391
Polymers18,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)220.236, 220.236, 220.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
31D
12A
22E
32G
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112B34 - 79
2112C34 - 79
3112D34 - 79
1212B81 - 199
2212C81 - 199
3212D81 - 199
1311B477
2311C477
3311D477
1122A34 - 79
2122E34 - 79
3122G34 - 79
4122H34 - 79
1222A81 - 166
2222E81 - 166
3222G81 - 166
4222H81 - 166
1322A168 - 170
2322E168 - 170
3322G168 - 170
4322H168 - 170
1422A172 - 199
2422E172 - 199
3422G172 - 199
4422H172 - 199

NCS ensembles :
ID
1
2

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Components

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


Mass: 18439.305 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline coronavirus / Strain: FIPV WSU-79/1146 / Gene: rep, 1a-1b / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q98VG9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 6.034559 Å3/Da / Density % sol: 79.617401 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: di-ammonium citrate, pH 6.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X13 / Wavelength: 0.812 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 4, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 3.9→20 Å / Num. all: 32610 / Num. obs: 32246 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.463 / Rsym value: 0.559 / Net I/σ(I): 4.45
Reflection shellResolution: 3.9→4.13 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4936 / Rsym value: 0.906 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata scaling
COMBATdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.91→19.94 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.167 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.867 / SU B: 29.747 / SU ML: 0.413 / SU Rfree: 0.54 / ESU R Free: 0.54 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 465 1.4 %RANDOM
Rwork0.199 ---
obs0.199 31727 99.8 %-
all-32192 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.88 Å2 / Biso mean: 31.085 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 3.91→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10384 0 111 0 10495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.02210669
X-RAY DIFFRACTIONr_angle_refined_deg2.6011.99214452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.88351336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.38724.643448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.264151880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0321556
X-RAY DIFFRACTIONr_chiral_restr0.1550.21712
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217793
X-RAY DIFFRACTIONr_mcbond_it0.8171.56640
X-RAY DIFFRACTIONr_mcangle_it1.637210712
X-RAY DIFFRACTIONr_scbond_it2.14734029
X-RAY DIFFRACTIONr_scangle_it3.8814.53740
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B696TIGHT POSITIONAL0.090.05
1C696TIGHT POSITIONAL0.10.05
1D696TIGHT POSITIONAL0.090.05
1B615MEDIUM POSITIONAL0.150.5
1C615MEDIUM POSITIONAL0.170.5
1D615MEDIUM POSITIONAL0.160.5
1B696TIGHT THERMAL0.130.5
1C696TIGHT THERMAL0.140.5
1D696TIGHT THERMAL0.120.5
1B615MEDIUM THERMAL0.152
1C615MEDIUM THERMAL0.142
1D615MEDIUM THERMAL0.122
2A652TIGHT POSITIONAL0.080.05
2E652TIGHT POSITIONAL0.050.05
2G652TIGHT POSITIONAL0.090.05
2H652TIGHT POSITIONAL0.080.05
2A605MEDIUM POSITIONAL0.110.5
2E605MEDIUM POSITIONAL0.070.5
2G605MEDIUM POSITIONAL0.120.5
2H605MEDIUM POSITIONAL0.130.5
2A652TIGHT THERMAL0.130.5
2E652TIGHT THERMAL0.060.5
2G652TIGHT THERMAL0.130.5
2H652TIGHT THERMAL0.120.5
2A605MEDIUM THERMAL0.132
2E605MEDIUM THERMAL0.072
2G605MEDIUM THERMAL0.132
2H605MEDIUM THERMAL0.132
LS refinement shellResolution: 3.907→4.004 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 33 -
Rwork0.234 2230 -
all-2263 -
obs--97.42 %

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