[English] 日本語
Yorodumi
- PDB-6wuu: Crystal structure of the SARS CoV-2 Papain-like protease in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wuu
TitleCrystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR250
Components
  • Non-structural protein 3
  • VIR250
KeywordsHydrolase/Hydrolase Inhibitor / COVID-19 / CORONAVIRUS / SARS / COV-2 / PAPAIN-LIKE PROTEASE / PLpro / deubiquitinating enzyme / ubiquitin / activity-based probe / Hydrolase-Hydrolase Inhibitor complex
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) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / 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) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / 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 / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / 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
Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / Jelly Rolls - #1680 / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / 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 ...Papain-like viral protease, N-terminal domain / Papain-like viral protease, thumb domain / Jelly Rolls - #1680 / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / 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.
Similarity search - Domain/homology
Papain-like protease peptide inhibitor VIR250 / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.79 Å
AuthorsLv, Z. / Olsen, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115568-05 United States
Citation
Journal: Sci Adv / Year: 2020
Title: Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti-COVID-19 drug design.
Authors: Rut, W. / Lv, Z. / Zmudzinski, M. / Patchett, S. / Nayak, D. / Snipas, S.J. / El Oualid, F. / Huang, T.T. / Bekes, M. / Drag, M. / Olsen, S.K.
#1: Journal: Biorxiv / Year: 2020
Title: Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design.
Authors: Rut, W. / Lv, Z. / Zmudzinski, M. / Patchett, S. / Nayak, D. / Snipas, S.J. / El Oualid, F. / Huang, T.T. / Bekes, M. / Drag, M. / Olsen, S.K.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 2, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com
Item: _entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name
Revision 1.4Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural protein 3
B: Non-structural protein 3
C: Non-structural protein 3
D: Non-structural protein 3
G: VIR250
H: VIR250
I: VIR250
J: VIR250
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,89016
Polymers150,5318
Non-polymers3598
Water32418
1
A: Non-structural protein 3
G: VIR250
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6983
Polymers37,6332
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-4 kcal/mol
Surface area15950 Å2
MethodPISA
2
B: Non-structural protein 3
H: VIR250
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7224
Polymers37,6332
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-10 kcal/mol
Surface area16240 Å2
MethodPISA
3
C: Non-structural protein 3
I: VIR250
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7224
Polymers37,6332
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-12 kcal/mol
Surface area15700 Å2
MethodPISA
4
D: Non-structural protein 3
J: VIR250
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7475
Polymers37,6332
Non-polymers1143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-27 kcal/mol
Surface area15890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.425, 189.693, 63.118
Angle α, β, γ (deg.)90.000, 98.660, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 1 through 501)
21(chain B and (resid 1 through 316 or resid 401 through 501))
31(chain C and (resid 1 through 316 or resid 401 through 501))
41(chain D and (resid 1 through 316 or resid 401 through 501))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 1 through 501)A1 - 501
211(chain B and (resid 1 through 316 or resid 401 through 501))B1 - 316
221(chain B and (resid 1 through 316 or resid 401 through 501))B401 - 501
311(chain C and (resid 1 through 316 or resid 401 through 501))C1 - 316
321(chain C and (resid 1 through 316 or resid 401 through 501))C401 - 501
411(chain D and (resid 1 through 316 or resid 401 through 501))D1 - 316
421(chain D and (resid 1 through 316 or resid 401 through 501))D401 - 501

-
Components

#1: Protein
Non-structural protein 3 / pp1ab / ORF1ab polyprotein / nsp3 / PL2-PRO / Papain-like protease / Papain-like proteinase / PL-PRO


Mass: 37128.145 Da / Num. of mol.: 4 / Fragment: UNP Residues 1563-1879
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, EC: 3.4.19.121, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein/peptide
VIR250


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 504.603 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Papain-like protease peptide inhibitor VIR250
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPeptide covalently linked to active site Cys
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→94.85 Å / Num. obs: 33589 / % possible obs: 99.6 % / Redundancy: 7.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.064 / Rrim(I) all: 0.17 / Net I/σ(I): 10.1 / Num. measured all: 237255
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.79-2.936.51.7882885244310.4370.7531.9441.199.1
9.25-94.8570.05866819530.9960.0230.06333.599.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W9C

6w9c


Resolution: 2.79→94.85 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 1992 5.95 %
Rwork0.1952 31489 -
obs0.1973 33481 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.66 Å2 / Biso mean: 80.9149 Å2 / Biso min: 39.04 Å2
Refinement stepCycle: final / Resolution: 2.79→94.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10122 0 152 18 10292
Biso mean--80.03 78.76 -
Num. residues----1274
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6127X-RAY DIFFRACTION9.555TORSIONAL
12B6127X-RAY DIFFRACTION9.555TORSIONAL
13C6127X-RAY DIFFRACTION9.555TORSIONAL
14D6127X-RAY DIFFRACTION9.555TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.79-2.860.33321290.32209233898
2.86-2.940.33941500.29932200235098
2.94-3.020.36451450.302322272372100
3.02-3.120.34231380.294322802418100
3.12-3.230.34051350.27122592394100
3.23-3.360.3081630.259822342397100
3.36-3.520.28581310.241722692400100
3.52-3.70.28071460.221622642410100
3.7-3.930.2681390.201622542393100
3.93-4.240.22611470.1812220236799
4.24-4.660.18451380.146122622400100
4.66-5.340.17131440.14822752419100
5.34-6.720.21261370.185922652402100
6.72-94.850.16421500.15862271242199
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0740.7623-0.39392.11661.1991-1.578-0.13640.20810.25490.16390.2460.18940.1818-0.065700.66270.0135-0.06410.6280.14590.449233.88696.4855.8221
20.12670.00210.42460.9617-0.17280.3373-0.08140.0353-0.37710.20820.0540.1069-0.30270.0547-00.7163-0.0499-0.00050.61330.01690.595636.487179.7692.7157
3-0.4135-0.971-0.15481.57440.25011.44830.03720.1369-0.0326-0.0616-0.11120.15330.06790.122400.42130.0183-0.03970.4899-0.01630.576738.760857.4777-9.2645
4-0.4119-1.49420.31791.3398-0.62240.43710.23610.2094-0.18910.33270.04220.0612-0.0398-0.074500.57670.02170.04460.53110.02790.627634.697161.30488.0518
50.64690.1217-0.10421.5218-0.02070.2679-0.27610.08030.4327-0.08620.11970.21290.031-0.25100.4324-0.0434-0.00330.50310.06680.475557.46378.0007-7.1631
60.0513-1.2325-0.87581.14281.0891.14030.06010.05150.111-0.0059-0.03610.04580.34040.0323-00.60220.0002-0.04460.40460.04880.40157.292731.23425.2611
70.45110.67160.20910.32970.86930.7278-0.1562-0.15090.10320.1111-0.05390.04460.0210.196-00.4778-0.0135-0.02460.5945-0.12080.494262.385546.385131.9179
80.1848-0.01530.69090.44750.27770.8377-0.05390.00540.1709-0.02120.0642-0.0719-0.05750.0349-00.54520.0054-0.0060.50910.0240.598857.322451.010214.04
91.03-0.0876-0.4350.0881-0.59680.22080.01130.0255-0.3223-0.1462-0.1995-0.0189-0.14270.056400.45970.1012-0.02340.5427-0.08160.57953.144384.7443-30.7822
100.91510.39380.00581.5542-1.07250.72640.02030.0396-0.1434-0.08490.03130.2241-0.12170.1969-00.5191-0.012-0.00830.4541-0.05820.515530.430876.9435-22.1187
110.7768-0.56861.2035-0.12840.15241.4204-0.0589-0.1051-0.0985-0.01660.31340.0006-0.1977-0.53700.60090.14790.12790.53390.1980.698510.776978.2374-1.865
120.5701-0.4563-0.3080.0926-0.39011.53220.00060.1214-0.1876-0.01020.10780.33660.1661-0.0552-00.49380.0219-0.06320.55710.07860.902911.365468.3419-18.7406
130.5215-1.3487-0.1981.16241.37470.21130.45-0.18330.2911-0.28130.0601-0.20670.15880.087500.4157-0.01510.0720.528-0.03160.495475.175910.905832.4781
141.9749-0.5197-0.7921.11290.61280.7682-0.1732-0.1571-0.11380.00070.11090.09170.13230.214100.48210.02860.01090.5890.02070.421253.176523.153232.2408
150.57470.55670.66480.08530.04391.19150.15570.2509-0.25630.0389-0.040.0755-0.1129-0.411800.51850.0307-0.02190.7813-0.12140.512134.216129.342312.5216
160.9892-0.44850.2385-0.25720.12231.17360.0670.11910.0080.18480.0410.04970.0567-0.244100.4218-0.06550.07310.6507-0.0020.517135.296429.975531.2419
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 120 )A3 - 120
2X-RAY DIFFRACTION2chain 'A' and (resid 121 through 175 )A121 - 175
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 253 )A176 - 253
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 316 )A254 - 316
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 62 )B3 - 62
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 181 )B63 - 181
7X-RAY DIFFRACTION7chain 'B' and (resid 182 through 238 )B182 - 238
8X-RAY DIFFRACTION8chain 'B' and (resid 239 through 319 )B239 - 319
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 61 )C3 - 61
10X-RAY DIFFRACTION10chain 'C' and (resid 62 through 174 )C62 - 174
11X-RAY DIFFRACTION11chain 'C' and (resid 175 through 253 )C175 - 253
12X-RAY DIFFRACTION12chain 'C' and (resid 254 through 313 )C254 - 313
13X-RAY DIFFRACTION13chain 'D' and (resid 3 through 77 )D3 - 77
14X-RAY DIFFRACTION14chain 'D' and (resid 78 through 175 )D78 - 175
15X-RAY DIFFRACTION15chain 'D' and (resid 176 through 253 )D176 - 253
16X-RAY DIFFRACTION16chain 'D' and (resid 254 through 315 )D254 - 315

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more