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Entry
Database: PDB / ID: 5rha
TitlePanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Z147647874 (Mpro-x2779)
Components3C-like proteinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / Transcription of SARS-CoV-2 sgRNAs / 5'-3' RNA helicase activity / mRNA cap binding complex / positive regulation of RNA biosynthetic process / Translation of Replicase and Assembly of the Replication Transcription Complex / Lyases; Phosphorus-oxygen lyases / Replication of the SARS-CoV-2 genome / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific peptidase activity / SARS coronavirus main proteinase / suppression by virus of host type I interferon production / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / protein K48-linked deubiquitination / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / 7-methylguanosine mRNA capping / RNA-templated transcription / viral transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell endoplasmic reticulum / suppression by virus of host toll-like receptor signaling pathway / host cell Golgi apparatus / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / positive stranded viral RNA replication / positive regulation of viral genome replication / suppression by virus of host TRAF-mediated signal transduction => GO:0039527 / helicase activity / protein autoprocessing / cysteine-type peptidase activity / ubiquitinyl hydrolase 1 / DNA helicase / cysteine-type deubiquitinase activity / DNA helicase activity / single-stranded RNA binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein processing / host cell perinuclear region of cytoplasm / viral protein processing / integral to membrane of host cell / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / endonuclease activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / host cell cytoplasm / DNA-templated transcription / protein dimerization activity / suppression by virus of host type I interferon-mediated signaling pathway / host cell nucleus / ATP hydrolysis activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Viral (Superfamily 1) RNA helicase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 15, middle domain, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus replicase NSP15, N-terminal oligomerization / Coronavirus proofreading exoribonuclease / Non-structural protein NSP15, middle domain superfamily / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / RNA polymerase, N-terminal, coronavirus / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / NSP1 globular domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Carbamoyl-phosphate synthase subdomain signature 2. / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Lipocalin signature. / : / : / : / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-M domain profile. / : / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / NSP1, globular domain, betacoronavirus / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / Coronavirus replicase NSP2, C-terminal / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / Non-structural protein 2, C-terminal domain, coronavirus / 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 / Non-structural protein NSP7, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / Coronavirus endopeptidase C30 / RNA synthesis protein NSP10, coronavirus / Coronavirus RNA synthesis protein NSP10 / Non-structural protein NSP8, coronavirus / Coronavirus replicase NSP8 / Coronavirus replicase NSP3, C-terminal / 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. / Non-structural protein NSP4, N-terminal, coronavirus
Similarity search - Domain/homology
Chem-T8M / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.51 Å
AuthorsFearon, D. / Owen, C.D. / Douangamath, A. / Lukacik, P. / Powell, A.J. / Strain-Damerell, C.M. / Resnick, E. / Krojer, T. / Gehrtz, P. / Wild, C. ...Fearon, D. / Owen, C.D. / Douangamath, A. / Lukacik, P. / Powell, A.J. / Strain-Damerell, C.M. / Resnick, E. / Krojer, T. / Gehrtz, P. / Wild, C. / Aimon, A. / Brandao-Neto, J. / Carbery, A. / Dunnett, L. / Skyner, R. / Snee, M. / London, N. / Walsh, M.A. / von Delft, F.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen
Authors: Fearon, D. / Owen, C.D. / Douangamath, A. / Lukacik, P. / Powell, A.J. / Strain-Damerell, C.M. / Resnick, E. / Krojer, T. / Gehrtz, P. / Wild, C. / Aimon, A. / Brandao-Neto, J. / Carbery, A. ...Authors: Fearon, D. / Owen, C.D. / Douangamath, A. / Lukacik, P. / Powell, A.J. / Strain-Damerell, C.M. / Resnick, E. / Krojer, T. / Gehrtz, P. / Wild, C. / Aimon, A. / Brandao-Neto, J. / Carbery, A. / Dunnett, L. / Skyner, R. / Snee, M. / London, N. / Walsh, M.A. / von Delft, F.
History
DepositionMay 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3626
Polymers33,8261
Non-polymers5375
Water6,287349
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,72512
Polymers67,6512
Non-polymers1,07410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4490 Å2
ΔGint1 kcal/mol
Surface area25320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.449, 52.773, 44.515
Angle α, β, γ (deg.)90.000, 103.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1331-

HOH

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Components

#1: Protein 3C-like proteinase / SARS-CoV-2 main protease


Mass: 33825.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-T8M / 1-{4-[(thiophen-2-yl)methyl]piperazin-1-yl}ethan-1-one


Mass: 224.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.9 Å3/Da / Density % sol: 35.34 % / Mosaicity: 0 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 15% PEG 4K, 5% DMSO, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.913 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.913 Å / Relative weight: 1
ReflectionResolution: 1.51→54.78 Å / Num. obs: 38077 / % possible obs: 95.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 20.74 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.058 / Rrim(I) all: 0.11 / Net I/σ(I): 6.2 / Num. measured all: 123165 / Scaling rejects: 90
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.51-1.542.41.277405817000.2090.9781.6230.785.7
8.27-54.783.80.03210172680.9990.0180.03724.399.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (29-NOV-2019)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6LU7
Resolution: 1.51→54.78 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.091 / SU Rfree Cruickshank DPI: 0.087
RfactorNum. reflection% reflectionSelection details
Rfree0.2095 1858 4.93 %RANDOM
Rwork0.1735 ---
obs0.1753 37676 94.2 %-
Displacement parametersBiso max: 76.37 Å2 / Biso mean: 23.99 Å2 / Biso min: 12.77 Å2
Baniso -1Baniso -2Baniso -3
1--5.1587 Å20 Å2-0.6943 Å2
2--0.3149 Å20 Å2
3---4.8438 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 1.51→54.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 31 349 2727
Biso mean--37.12 34.49 -
Num. residues----304
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d828SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes424HARMONIC5
X-RAY DIFFRACTIONt_it2443HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion315SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2732SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2443HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3319HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion14.42
LS refinement shellResolution: 1.51→1.52 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3153 43 5.7 %
Rwork0.2326 711 -
all-754 -
obs--85.65 %
Refinement TLS params.Method: refined / Origin x: 11.8153 Å / Origin y: 0.5882 Å / Origin z: 4.8963 Å
111213212223313233
T-0.0393 Å2-0.0031 Å2-0.0104 Å2--0.0069 Å2-0.0205 Å2---0.0337 Å2
L0.3368 °20.1035 °2-0.0024 °2-0.863 °2-0.7195 °2--0.5451 °2
S-0.0538 Å °0.0117 Å °-0.0221 Å °-0.0303 Å °0.0577 Å °-0.0406 Å °0.0056 Å °-0.0289 Å °-0.0039 Å °
Refinement TLS groupSelection details: { A|* }

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