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- PDB-7aku: Structure of SARS-CoV-2 Main Protease bound to Calpeptin. -

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Basic information

Entry
Database: PDB / ID: 7aku
TitleStructure of SARS-CoV-2 Main Protease bound to Calpeptin.
Components3C-like proteinase
KeywordsPEPTIDE BINDING PROTEIN / SARS-CoV-2 / mPro / COVID-!9
Function / homology
Function and homology information


Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / 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 / modulation by virus of host autophagy / RNA phosphodiester bond hydrolysis, exonucleolytic / mRNA methylation ...Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / 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 / modulation by virus of host autophagy / RNA phosphodiester bond hydrolysis, exonucleolytic / 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 / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / suppression by virus of host toll-like receptor signaling pathway / protein K48-linked deubiquitination / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / transcription, RNA-templated / protein K63-linked deubiquitination / positive stranded viral RNA replication / protein autoprocessing / viral genome replication / cysteine-type peptidase activity / suppression by virus of host TRAF activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / helicase activity / ubiquitinyl hydrolase 1 / Transferases; Transferring one-carbon groups; Methyltransferases / viral transcription / DNA helicase / methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / thiol-dependent deubiquitinase / 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 / suppression by virus of host type I interferon-mediated signaling pathway / viral protein processing / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / transcription, DNA-templated / Hydrolases; Acting on ester bonds / 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 Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus SUD-C domain / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein NSP1 superfamily, betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronaviral / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus proofreading exoribonuclease / Coronavirus replicase NSP15, middle domain / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus 2'-O-methyltransferase / Coronavirus replicase NSP15, N-terminal oligomerisation / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Betacoronavirus Nsp3c-M domain profile. / Coronaviridae zinc-binding (CV ZBD) domain profile. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP1, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein 6, betacoronavirus / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAR) / 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. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Non-structural protein NSP3A domain-like superfamily / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Lipocalin signature. / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein NSP7 superfamily, coronavirus / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Peptidase family C16 domain profile. / Coronavirus endopeptidase C30 / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / 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 / Coronavirus papain-like peptidase / Coronavirus replicase NSP4, N-terminal / Papain-like viral protease, palm and finger domains, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP8, coronavirus-like / Peptidase C16, coronavirus / Peptidase C30, coronavirus / Peptidase C30, domain 3, coronavirus
Similarity search - Domain/homology
Calpeptin / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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. / Falke, S. / Alves Franca, B. / Schwinzer, M. / Brognaro, H. / Werner, N. / 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. / 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, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2056 - project ID 390715994 Germany
European CommissionEU project 101003551 - EXSCALATE4CoV (E4C)European Union
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
DepositionOct 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 9, 2020Group: Database references / Category: citation_author
Revision 2.0Apr 14, 2021Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq
Item: _entity.formula_weight / _entity.pdbx_description ..._entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1May 19, 2021Group: Database references / Category: citation / citation_author
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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)34,2253
Polymers33,8261
Non-polymers4002
Water1,58588
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4516
Polymers67,6512
Non-polymers8004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3310 Å2
ΔGint-33 kcal/mol
Surface area24480 Å2
Unit cell
γ
α
β
Length a, b, c (Å)114.667, 53.843, 45.115
Angle α, β, γ (deg.)90.000, 101.857, 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

21A-566-

HOH

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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-RN2 / Calpeptin


Mass: 364.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 291 K / Method: counter-diffusion
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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.491→56.11 Å / Num. obs: 5686 / % possible obs: 86.23 % / Redundancy: 3.75 % / Biso Wilson estimate: 33.85 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.19 / Rrim(I) all: 0.221 / Net I/σ(I): 3.712
Reflection shellResolution: 2.491→2.815 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 1.076 / Num. unique obs: 285 / CC1/2: 0.5782 / % possible all: 48.55

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
REFMACphasing
STARANISOdata scaling
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YVF
Resolution: 2.5→19.56 Å / SU ML: 0.0896 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.8598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 294 5.19 %
Rwork0.1823 5366 -
obs0.1853 5660 60.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.63 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 27 88 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862447
X-RAY DIFFRACTIONf_angle_d0.82633326
X-RAY DIFFRACTIONf_chiral_restr0.0463374
X-RAY DIFFRACTIONf_plane_restr0.0047434
X-RAY DIFFRACTIONf_dihedral_angle_d20.5041872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-3.150.3612580.2396993X-RAY DIFFRACTION22.47
3.15-19.560.21982360.17524373X-RAY DIFFRACTION97.01
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)
11.14957012923-0.8185138588061.261322917161.88663203759-1.369103093761.517512029040.143567391598-0.440712922317-0.3556926585370.3603515413620.2598896389070.596561577278-0.0833634837446-0.5143518741640.8534423427310.361096871046-0.09054474243570.08297766876570.316633538120.1022621312290.08611166296547.88938924027-10.64167509379.8939576001
21.109068333830.3644281100541.3044118371.39007665650.5708999394081.880615570870.15586806318-0.62686796579-0.3760608724890.195563991837-0.3624756808890.08554640416030.154471763354-0.724228160039-0.3147530597370.478416251737-0.0664880948390.09082920593620.3964754255920.1418438216170.38103709920815.3168621902-14.89194981423.5869674226
32.50127000803-0.6566480739570.6466077302971.26438196491-1.339055410741.636098518380.05029534324280.2607490631480.07395460568360.0371256560573-0.0441367451665-0.107141313109-0.007199642406760.0711939530270.001490707385050.199897489351-0.02289343846160.002480697542120.189607634898-0.02513367090380.17004094082812.1629961264-4.256896170878.4359882776
42.43775143393-0.694139868764-0.5716549593980.9276402141610.6358431109421.82085887660.03970397507430.3066370734030.508341430238-0.1809167215020.01312310679190.02873622527380.113260727631-0.2359332902840.0001232370876910.315357366481-0.01731217706130.004814790938560.398491569720.1638480960190.45123427347612.572359436915.4771949837-8.86914815729
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 43 )1 - 431 - 43
22chain 'A' and (resid 44 through 90 )44 - 9044 - 90
33chain 'A' and (resid 91 through 190 )91 - 19091 - 192
44chain 'A' and (resid 191 through 305 )191 - 305193 - 307

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