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- PDB-7mhl: Ensemble refinement structure of SARS-CoV-2 main protease (Mpro) ... -

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Basic information

Entry
Database: PDB / ID: 7mhl
TitleEnsemble refinement structure of SARS-CoV-2 main protease (Mpro) at 100 K
Components3C-like proteinase
KeywordsHYDROLASE / SARS-CoV-2 / Coronavirus / main protease / 3CLpro / Mpro / ensemble refinement / temperature series / temperature / multitemperature
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / SARS coronavirus main proteinase / forked DNA-dependent helicase activity / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / four-way junction helicase activity / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / SARS-CoV-2 modulates host translation machinery / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / regulation of autophagy / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / 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 / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) 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 / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsEbrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133769 United States
Department of Energy (DOE, United States)National Virtual Biotechnology Laboratory (NVBL) United States
Department of Energy (DOE, United States)Coronavirus CARES Act United States
Department of Energy (DOE, United States)BNL LDRD 20-042 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
Department of Energy (DOE, United States)KP1605010 United States
Citation
Journal: Iucrj / Year: 2022
Title: The tem-per-ature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).
Authors: Ebrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A.
#1: Journal: Biorxiv / Year: 2021
Title: The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).
Authors: Ebrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A.
#2: Journal: Iucrj / Year: 2022
Title: The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro)
Authors: Ebrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A.
#3: Journal: Biorxiv / Year: 2021
Title: The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).
Authors: Ebrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A.
History
DepositionApr 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 2.0Apr 6, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp / citation_author / database_2 / database_PDB_caveat / entity / entity_src_gen / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_polymer_linkage / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_ls_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_keywords / struct_sheet_range / struct_site / struct_site_gen
Item: _citation_author.identifier_ORCID / _database_2.pdbx_DOI ..._citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_caveat.text / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _software.version / _struct.title / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_keywords.text / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id
Description: Ligand identity
Details: X-ray fluorescence is consistent with the presence of Zn.
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Revision 2.2Sep 14, 2022Group: Database references / Category: citation / citation_author
Revision 2.3Mar 8, 2023Group: Database references / Category: citation / citation_author
Revision 2.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)34,2827
Polymers33,8261
Non-polymers4566
Water3,423190
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,56314
Polymers67,6512
Non-polymers91212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4420 Å2
ΔGint-9 kcal/mol
Surface area27170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.706, 53.320, 44.567
Angle α, β, γ (deg.)90.000, 102.960, 90.000
Int Tables number5
Space group name H-MC121
Number of models54
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

23A-531-

HOH

33A-537-

HOH

44A-545-

HOH

54A-645-

HOH

65A-510-

HOH

75A-554-

HOH

86A-567-

HOH

96A-621-

HOH

107A-507-

HOH

117A-653-

HOH

128A-503-

HOH

138A-571-

HOH

148A-592-

HOH

158A-636-

HOH

169A-583-

HOH

179A-592-

HOH

189A-632-

HOH

199A-650-

HOH

2010A-552-

HOH

2110A-557-

HOH

2210A-600-

HOH

2311A-544-

HOH

2411A-557-

HOH

2511A-633-

HOH

2612A-565-

HOH

2712A-573-

HOH

2812A-679-

HOH

2913A-634-

HOH

3013A-652-

HOH

3114A-598-

HOH

3214A-640-

HOH

3315A-530-

HOH

3416A-564-

HOH

3516A-666-

HOH

3617A-520-

HOH

3717A-668-

HOH

3818A-553-

HOH

3918A-629-

HOH

4018A-654-

HOH

4119A-539-

HOH

4219A-540-

HOH

4319A-589-

HOH

4420A-524-

HOH

4521A-513-

HOH

4621A-646-

HOH

4722A-587-

HOH

4822A-637-

HOH

4923A-623-

HOH

5023A-666-

HOH

5124A-577-

HOH

5224A-655-

HOH

5325A-597-

HOH

5425A-603-

HOH

5526A-583-

HOH

5626A-591-

HOH

5726A-674-

HOH

5827A-629-

HOH

5927A-641-

HOH

6028A-557-

HOH

6129A-507-

HOH

6229A-640-

HOH

6330A-541-

HOH

6431A-674-

HOH

6532A-635-

HOH

6633A-536-

HOH

6733A-551-

HOH

6833A-674-

HOH

6934A-600-

HOH

7035A-519-

HOH

7135A-579-

HOH

7236A-520-

HOH

7336A-610-

HOH

7436A-623-

HOH

7537A-501-

HOH

7637A-530-

HOH

7737A-655-

HOH

7838A-648-

HOH

7938A-662-

HOH

8039A-543-

HOH

8139A-613-

HOH

8240A-531-

HOH

8340A-661-

HOH

8441A-513-

HOH

8541A-537-

HOH

8641A-555-

HOH

8742A-515-

HOH

8842A-629-

HOH

8943A-552-

HOH

9043A-556-

HOH

9143A-581-

HOH

9244A-503-

HOH

9344A-610-

HOH

9444A-637-

HOH

9545A-646-

HOH

9647A-506-

HOH

9748A-578-

HOH

9849A-609-

HOH

9950A-512-

HOH

10050A-660-

HOH

10151A-567-

HOH

10251A-661-

HOH

10352A-507-

HOH

10452A-642-

HOH

10553A-521-

HOH

10653A-551-

HOH

10754A-624-

HOH

10854A-668-

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 / Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.95 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 22% PEG4000, 100 mM HEPES, pH 7.0, 3-5% DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5477→48.047 Å / Num. obs: 37901 / % possible obs: 99.7185 % / Redundancy: 3.3653 % / CC1/2: 0.9769 / Rmerge(I) obs: 0.1579 / Rpim(I) all: 0.1004 / Rrim(I) all: 0.1876 / Net I/σ(I): 3.2643 / Num. measured all: 127548
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.5477-1.574495.95593.39520.50741.0276620318270.69480.32480.6044
1.5744-1.603199.73453.40360.47731.113639218780.73820.30330.5672
1.6031-1.63391003.36860.45881.1926627918640.72340.29460.5472
1.6339-1.667299.9473.32130.43021.3178626418860.73270.27850.5141
1.6672-1.703599.94783.27310.39751.5079626819150.73770.25910.476
1.7035-1.743199.94683.10370.37141.6182583518800.77140.25040.4494
1.7431-1.78671003.30850.34541.8623633919160.80470.22350.4127
1.7867-1.83599.89213.24510.31862.1269601018520.81460.20640.3807
1.835-1.88999.89423.33740.31522.4798630118880.82640.20020.3744
1.889-1.9599.47153.52230.28282.978662918820.86380.17470.3331
1.95-2.01971003.47980.26363.3583662219030.88320.16420.3112
2.0197-2.10061003.4620.24533.7137660919090.8920.1530.2897
2.1006-2.19621003.42240.23414.0265637618630.90560.14690.277
2.1962-2.311999.89693.32990.21674.2126645019370.89410.13910.2583
2.3119-2.456899.89353.1610.19794.271593018760.910.13150.2384
2.4568-2.64651003.32430.1774.6905635619120.93290.1150.2117
2.6465-2.912899.94733.53350.1645.3012669618950.94480.10180.1934
2.9128-3.33421003.58630.1445.9356690019240.95990.08870.1695
3.3342-4.200399.9483.40760.12566.2065654619210.96120.07970.1492
4.2003-48.070299.89873.31630.09825.986654319730.97740.06380.1175

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.ensemble_refinement:1.19.2_4158)refinement
xia20.5.902-gffa11588-dials-1.14data reduction
DIALS1.14.13-g10ecfbb15-releasedata scaling
PHASER1.18.2_3874phasing
PDB_EXTRACT3.28data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YB7

6yb7


Resolution: 1.55→48.047 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2272 --
Rwork0.1658 --
obs0.1689 37898 99.71 %
Refinement stepCycle: final / Resolution: 1.55→48.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 0 0 2367
Num. residues----0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.590.29231410.225248397
1.59-1.630.29481430.2082520100
1.63-1.680.27651420.20312590100
1.68-1.730.26431480.19082542100
1.73-1.790.26531270.18322588100
1.79-1.870.3141120.19142575100
1.87-1.950.26981260.18372550100
1.95-2.050.25011350.17962591100
2.05-2.180.25791330.18062578100
2.18-2.350.2241420.16272553100
2.35-2.590.23011430.15722582100
2.59-2.960.20931480.1512578100
2.96-3.730.19971300.15592596100
3.73-48.0470.18621360.14752666100

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