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- PDB-7aga: Structure of SARS-CoV-2 Main Protease bound to AT7519 -

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Basic information

Entry
Database: PDB / ID: 7aga
TitleStructure of SARS-CoV-2 Main Protease bound to AT7519
Components3C-like proteinase
KeywordsHYDROLASE / SARS-CoV-2 / MPro / COVID-19 / PEPTIDE BINDING PROTEIN / virus protease
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / host cell Golgi apparatus / Replication of the SARS-CoV-2 genome / suppression by virus of host type I interferon production / host cell endoplasmic reticulum / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / G-quadruplex RNA binding / 3'-5'-exoribonuclease activity / suppression by virus of host ISG15-protein conjugation / host cell endoplasmic reticulum-Golgi intermediate compartment / protein K48-linked deubiquitination / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transcription, RNA-templated / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / positive stranded viral RNA replication / protein autoprocessing / cysteine-type peptidase activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / viral genome replication / suppression by virus of host TRAF activity / helicase activity / viral transcription / Transferases; Transferring one-carbon groups; Methyltransferases / ubiquitinyl hydrolase 1 / methyltransferase activity / DNA helicase / thiol-dependent deubiquitinase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / DNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / methylation / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / viral protein processing / suppression by virus of host type I interferon-mediated signaling pathway / Hydrolases; Acting on ester bonds / transcription, DNA-templated / host cell cytoplasm / protein dimerization activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Non-structural protein NSP15, middle domain superfamily / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / RNA polymerase, N-terminal, coronavirus / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP1 superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP1, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Non-structural protein 6, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Lipocalin signature. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Peptidase family C16 domain profile. / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP7 / Coronavirus endopeptidase C30 / Non-structural protein NSP8, coronavirus-like / RNA synthesis protein NSP10, coronavirus / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP6 / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / Coronavirus replicase NSP4, N-terminal / Non-structural protein NSP8 superfamily, coronavirus / Peptidase C30, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Coronavirus replicase NSP3, C-terminal
Similarity search - Domain/homology
Chem-LZE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsGuenther, S. / Reinke, P. / Oberthuer, D. / Yefanov, O. / Gelisio, L. / Ginn, H. / Lieske, J. / Domaracky, M. / Brehm, W. / Rahmani Mashour, A. ...Guenther, S. / Reinke, P. / Oberthuer, D. / Yefanov, O. / Gelisio, L. / Ginn, H. / Lieske, J. / Domaracky, M. / Brehm, W. / Rahmani Mashour, A. / White, T.A. / Knoska, J. / Pena Esperanza, G. / Koua, F. / Tolstikova, A. / Groessler, M. / Fischer, P. / Hennicke, V. / Fleckenstein, H. / Trost, F. / Galchenkova, M. / Gevorkov, Y. / Li, C. / Awel, S. / Paulraj, L.X. / Ullah, N. / Andaleeb, H. / Werner, N. / Falke, S. / Hinrichs, W. / Alves Franca, B. / Schwinzer, M. / Brognaro, H. / Perbandt, M. / Tidow, H. / Seychell, B. / Beck, T. / Meier, S. / Doyle, J.J. / Giseler, H. / Melo, D. / Dunkel, I. / Lane, T.J. / Peck, A. / Saouane, S. / Hakanpaeae, J. / Meyer, J. / Noei, H. / Boger, J. / Gribbon, P. / Ellinger, B. / Kuzikov, M. / Wolf, M. / Zhang, L. / Ehrt, C. / Pletzer-Zelgert, J. / Wollenhaupt, J. / Feiler, C. / Weiss, M. / Schulz, E.C. / Mehrabi, P. / Norton-Baker, B. / Schmidt, C. / Lorenzen, K. / Schubert, R. / Han, H. / Chari, A. / Fernandez Garcia, Y. / Turk, D. / Hilgenfeld, R. / Rarey, M. / Zaliani, A. / Chapman, H.N. / Pearson, A. / Betzel, C. / Meents, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2056 - project ID 390715994 Germany
European CommissionEU project 101003551 - EXSCALATE4CoV (E4C) Germany
Citation
Journal: Science / Year: 2021
Title: X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease.
Authors: Gunther, S. / Reinke, P.Y.A. / Fernandez-Garcia, Y. / Lieske, J. / Lane, T.J. / Ginn, H.M. / Koua, F.H.M. / Ehrt, C. / Ewert, W. / Oberthuer, D. / Yefanov, O. / Meier, S. / Lorenzen, K. / ...Authors: Gunther, S. / Reinke, P.Y.A. / Fernandez-Garcia, Y. / Lieske, J. / Lane, T.J. / Ginn, H.M. / Koua, F.H.M. / Ehrt, C. / Ewert, W. / Oberthuer, D. / Yefanov, O. / Meier, S. / Lorenzen, K. / Krichel, B. / Kopicki, J.D. / Gelisio, L. / Brehm, W. / Dunkel, I. / Seychell, B. / Gieseler, H. / Norton-Baker, B. / Escudero-Perez, B. / Domaracky, M. / Saouane, S. / Tolstikova, A. / White, T.A. / Hanle, A. / Groessler, M. / Fleckenstein, H. / Trost, F. / Galchenkova, M. / Gevorkov, Y. / Li, C. / Awel, S. / Peck, A. / Barthelmess, M. / Schlunzen, F. / Lourdu Xavier, P. / Werner, N. / Andaleeb, H. / Ullah, N. / Falke, S. / Srinivasan, V. / Franca, B.A. / Schwinzer, M. / Brognaro, H. / Rogers, C. / Melo, D. / Zaitseva-Doyle, J.J. / Knoska, J. / Pena-Murillo, G.E. / Mashhour, A.R. / Hennicke, V. / Fischer, P. / Hakanpaa, J. / Meyer, J. / Gribbon, P. / Ellinger, B. / Kuzikov, M. / Wolf, M. / Beccari, A.R. / Bourenkov, G. / von Stetten, D. / Pompidor, G. / Bento, I. / Panneerselvam, S. / Karpics, I. / Schneider, T.R. / Garcia-Alai, M.M. / Niebling, S. / Gunther, C. / Schmidt, C. / Schubert, R. / Han, H. / Boger, J. / Monteiro, D.C.F. / Zhang, L. / Sun, X. / Pletzer-Zelgert, J. / Wollenhaupt, J. / Feiler, C.G. / Weiss, M.S. / Schulz, E.C. / Mehrabi, P. / Karnicar, K. / Usenik, A. / Loboda, J. / Tidow, H. / Chari, A. / Hilgenfeld, R. / Uetrecht, C. / Cox, R. / Zaliani, A. / Beck, T. / Rarey, M. / Gunther, S. / Turk, D. / Hinrichs, W. / Chapman, H.N. / Pearson, A.R. / Betzel, C. / Meents, A.
#1: Journal: Biorxiv / Year: 2020
Title: Inhibition of SARS-CoV-2 main protease by allosteric drug-binding
Authors: Guenther, S. / Reinke, P.Y.A., / Fernandez-Garcia, Y., / Lieske, J., / Lane, T.J., / Ginn, H.M., / Koua, F.H.M., / Ehrt, C., / Ewert, W., / Oberthuer, D., / Yefanov, O., / Meier, S., / ...Authors: Guenther, S. / Reinke, P.Y.A., / Fernandez-Garcia, Y., / Lieske, J., / Lane, T.J., / Ginn, H.M., / Koua, F.H.M., / Ehrt, C., / Ewert, W., / Oberthuer, D., / Yefanov, O., / Meier, S., / Lorenzen, K., / Krichel, B., / Kopicki, J.D., / Gelisio, L., / Brehm, W., / Dunkel , I., / Seychell , B., / Gieseler , H., / Norton-Baker , B., / Escudero-Perez, B., / Domaracky , M., / Saouane, S., / Tolstikova , A., / White, T.A., / Hanle, A., / Groessler , M., / Fleckenstein , H., / Trost , F., / Galchenkova , M., / Gevorkov , Y., / Li , C., / Awel , S., / Peck, A. / Barthelmess , M., / Schluenzen , F., / Paulraj , L.X., / Werner , N., / Andaleeb , H., / Ullah , N., / Falke , S., / Srinivasan, V., / Franca , B., / Schwinzer , M., / Brognaro , H., / Rogers , C., / Melo , D., / Doyle , J.J., / Knoska , J., / Pena Murillo, G.E., / Rahmani Mashhour, A., / Guicking , F., / Hennicke , V., / Fischer , P., / Hakanpaeae , J., / Meyer , J., / Gribbon , P., / Ellinger , B., / Kuzikov , M., / Wolf , M., / Burenkov, G., / von Stetten, D., / Pompidor, G., / Bento, I., / Panneerselvam, S., / Karpics, I., / Schneider , T.R., / Garcia Alai, M., / Niebling, S., / Guenther , C., / Schmidt , C., / Schubert , R., / Han , H., / Boger, J., / Monteiro , D., / Zhang, L., / Sun, X., / Pletzer-Zelgert , J., / Wollenhaupt , J., / Feiler , C., / Weiss , M., / Schulz , E.C., / Mehrabi , P., / Karnicar , K., / Usenik, A., / Loboda , J., / Tidow , H., / Chari , A., / Hilgenfeld , R., / Uetrecht , C., / Cox , R., / Zaliani , A., / Beck , T., / Rarey , M., / Guenther , S., / Turk , D., / Hinrichs , W., / Chapman , H.N., / Pearson , A., / Betzel , C., / Meents , A.
History
DepositionSep 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation_author
Revision 2.0Apr 14, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / entity_name_com / entity_src_gen / pdbx_nonpoly_scheme / pdbx_refine_tls_group / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_refine_tls_group.selection_details
Revision 2.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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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)34,90412
Polymers33,8261
Non-polymers1,07811
Water4,125229
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,80824
Polymers67,6512
Non-polymers2,15622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6400 Å2
ΔGint-23 kcal/mol
Surface area25550 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)112.372, 52.641, 44.585
Angle α, β, γ (deg.)90.000, 102.673, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-402-

CL

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


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-LZE / 4-{[(2,6-dichlorophenyl)carbonyl]amino}-N-piperidin-4-yl-1H-pyrazole-3-carboxamide


Mass: 382.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17Cl2N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 35.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Co-crystallization with the compound was achieved by equlibrating a 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl against a ...Details: Co-crystallization with the compound was achieved by equlibrating a 6.25 mg/ml protein solution in 20 mM HEPES buffer (pH 7.8) containing 1 mM DTT, 1mM EDTA, and 150 mM NaCl against a reservoir solution of 100 mM MIB buffer (2:3:3 molar ratio of malonic acid, imidazole, and boric acid), pH 7.5, containing 25% v/v PEG 1500 and 5% v/v DMSO. Prior to crystallization compound solutions in DMSO were dried onto the wells of SwissCI 96-well plates. To achieve reproducible crystal growth seeding was used. Crystals appeared within a few hours and reached their final size after 2 -3 days. Crystals were manually harvested and flash cooled in liquid nitrogen for subsequent X-ray diffraction data collection.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.003 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.003 Å / Relative weight: 1
ReflectionResolution: 1.68→30.93 Å / Num. obs: 28529 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 27.99 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.01
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.62 / Num. unique obs: 4605 / CC1/2: 0.231 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.13-2998_9999refinement
REFMAC5.8.0222refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YB7
Resolution: 1.68→30.93 Å / SU ML: 0.311 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.4548 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2225 1426 5 %
Rwork0.1858 27103 -
obs0.1877 28529 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.97 Å2
Refinement stepCycle: LAST / Resolution: 1.68→30.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2358 0 59 229 2646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092613
X-RAY DIFFRACTIONf_angle_d0.76073562
X-RAY DIFFRACTIONf_chiral_restr0.0491393
X-RAY DIFFRACTIONf_plane_restr0.0059464
X-RAY DIFFRACTIONf_dihedral_angle_d10.83051553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.740.42731440.3812740X-RAY DIFFRACTION99.83
1.74-1.810.371450.34292745X-RAY DIFFRACTION99.55
1.81-1.890.34751440.30312741X-RAY DIFFRACTION99.93
1.89-1.990.2981430.26882730X-RAY DIFFRACTION99.45
1.99-2.120.27661450.22082746X-RAY DIFFRACTION99.76
2.12-2.280.22981450.19352746X-RAY DIFFRACTION99.79
2.28-2.510.20851440.17952753X-RAY DIFFRACTION99.97
2.51-2.870.23861460.17642774X-RAY DIFFRACTION99.52
2.87-3.620.21191300.15512451X-RAY DIFFRACTION88.27
3.62-30.930.16281400.14772677X-RAY DIFFRACTION94.44
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.658238544290.270926079698-0.03802489081831.319753820790.2248575168320.5213809249730.00993540006768-0.0329135885292-0.0637830113264-0.0277443230289-0.02735016751930.09410419999360.1290041317390.0371697067281-3.98059220094E-50.2066604113630.0002761870384090.006259237971990.201316620086-0.005457729347440.2385920998327.68635599145-10.61426309249.9203725455
21.632230635930.1617838755331.242008747852.45525089915-0.5014535459051.246490286790.0956935006316-0.167730138505-0.2102677556390.273827348798-0.0555331875066-0.2147533106980.169010060831-0.036219349943-2.77560975783E-50.2449119183920.01547870589390.02826343482650.2690537819540.01330436314190.25737834959614.8602588418-14.227152507217.4834043391
30.59822236672-0.31251762950.4444935003371.57325398382-1.515561382381.58485825423-0.04637980530540.00279872342980.006092555164080.0198518285097-0.00747222338312-0.0832779294937-0.06490655046860.07109578015966.71280836575E-50.205199673655-0.003191107609470.008321780436930.203575038429-0.00794793593270.22163623848211.48556454250.7949233697746.85676703015
43.16099877972-0.0290754445338-0.4993919310911.52825380256-0.2853476876292.709375991680.01638298881680.08985053430940.168075735332-0.02558054305730.001509531293020.0153155837036-0.173413266961-0.165164271765-0.0009055898409120.233062387953-0.0180578224431-0.01253411790510.2324263487010.02106160719490.21021116215812.692711344416.1930416162-9.73121797872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 214 )
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 305 )

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