[English] 日本語
Yorodumi
- PDB-5tl7: Crystal structure of SARS-CoV papain-like protease in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tl7
TitleCrystal structure of SARS-CoV papain-like protease in complex with C-terminal domain mouse ISG15
Components
  • Replicase polyprotein 1ab
  • Ubiquitin-like protein ISG15
KeywordsSignaling protein/Hydrolase / Signaling protein / Hydrolase / Signaling protein-Hydrolase complex
Function / homology
Function and homology information


positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein localization to mitochondrion ...positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein localization to mitochondrion / response to type I interferon / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / negative regulation of type I interferon-mediated signaling pathway / K63-linked deubiquitinase activity / negative regulation of viral genome replication / SARS-CoV-1 modulates host translation machinery / viral transcription / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / response to bacterium / response to virus / modification-dependent protein catabolic process / protein tag activity / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of type II interferon production / integrin binding / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / : / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / defense response to virus / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / defense response to bacterium / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / innate immune response / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ubiquitin protein ligase binding / ATP hydrolysis activity / proteolysis / zinc ion binding / extracellular region / ATP binding / membrane / identical protein binding / cytoplasm
Similarity search - Function
Papain-like viral protease, N-terminal domain / Jelly Rolls - #1680 / Papain-like viral protease, thumb domain / : / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / Ubiquitin family / RNA-dependent RNA polymerase, SARS-CoV-like ...Papain-like viral protease, N-terminal domain / Jelly Rolls - #1680 / Papain-like viral protease, thumb domain / : / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 / Ubiquitin-like (UB roll) / Ubiquitin family / RNA-dependent RNA polymerase, SARS-CoV-like / Ubiquitin homologues / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Ubiquitin-like domain / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Ubiquitin domain profile. / (+) 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 / Coronavirus 3Ecto domain profile. / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab / Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesMus musculus (house mouse)
SARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsDaczkowski, C.D. / Dzimianski, J.V. / Pegan, S.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI109008 United States
United States Department of Agriculture (USDA)58-5030-5-034 United States
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species.
Authors: Daczkowski, C.M. / Dzimianski, J.V. / Clasman, J.R. / Goodwin, O. / Mesecar, A.D. / Pegan, S.D.
History
DepositionOct 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-like protein ISG15
B: Replicase polyprotein 1ab
C: Ubiquitin-like protein ISG15
D: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3116
Polymers90,1814
Non-polymers1312
Water2,198122
1
A: Ubiquitin-like protein ISG15
B: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1563
Polymers45,0902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin-like protein ISG15
D: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1563
Polymers45,0902
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.981, 98.191, 106.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein


Mass: 9280.692 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 78-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Isg15, G1p2, Ucrp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q64339
#2: Protein Replicase polyprotein 1ab / pp1ab / ORF1ab polyprotein


Mass: 35809.629 Da / Num. of mol.: 2 / Fragment: UNP residues 1541-1855
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0C6X7, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, RNA-directed RNA polymerase, DNA ...References: UniProt: P0C6X7, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Transferases; Transferring one-carbon groups; Methyltransferases, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 65% (v/v) MPD, 0.1 M Tris [pH 8.0], supplemented with 30% (w/v) Trimethylamine N-oxide dihydrate additive in a 1:5 dilution

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.44→72.23 Å / Num. obs: 29922 / % possible obs: 99.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 18
Reflection shellResolution: 2.44→2.53 Å / Rmerge(I) obs: 0.742

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E9S,5JZE

3e9s

5jze


Resolution: 2.44→72.23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.905 / SU B: 24.002 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.697 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26744 1529 5.1 %RANDOM
Rwork0.19211 ---
obs0.19615 28405 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.266 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.44→72.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6226 0 2 122 6350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196362
X-RAY DIFFRACTIONr_bond_other_d0.0010.026006
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9518602
X-RAY DIFFRACTIONr_angle_other_deg0.754313822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.39524.364291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.493151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.281528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021495
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0093.5093120
X-RAY DIFFRACTIONr_mcbond_other2.0083.5093119
X-RAY DIFFRACTIONr_mcangle_it2.9575.263893
X-RAY DIFFRACTIONr_mcangle_other2.9585.2613894
X-RAY DIFFRACTIONr_scbond_it2.4763.7843242
X-RAY DIFFRACTIONr_scbond_other2.4763.7843243
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8115.5674710
X-RAY DIFFRACTIONr_long_range_B_refined6.4128.1866933
X-RAY DIFFRACTIONr_long_range_B_other6.4128.1236917
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.442→2.506 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 118 -
Rwork0.263 1983 -
obs--96.6 %
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)
112.5229-3.7431-7.69877.00575.289210.67310.2448-0.29070.92630.24670.0449-0.2775-0.22910.0127-0.28960.35830.0238-0.05480.16040.02360.226-34.6124.17436.5
28.1204-1.40476.89571.1784-1.658322.11280.46661.17230.0733-0.0605-0.34230.10220.43210.3199-0.12420.43740.0344-0.01360.3239-0.010.2834-24.761115.83726.756
38.065-3.3124-12.946211.06621.073430.44050.92920.20960.2298-0.5522-0.46590.1787-0.7624-0.2081-0.46320.2904-0.018-0.03560.2588-0.00230.1741-35.345119.60632.436
42.0357-0.2247-2.54045.12753.4386.4802-0.1487-0.287-0.1550.0774-0.00670.43170.10210.09570.15540.29060.03380.00050.23160.03850.2372-33.57117.64144.355
59.9527-0.7030.70167.4284-0.1978.34720.21880.035-0.2445-0.418-0.39690.61520.3177-0.67080.17810.3421-0.0108-0.09020.2628-0.08880.3082-34.7110.99134.753
66.0304-5.9165-0.28217.02022.67996.0870.12290.0111-0.21820.0720.0747-0.13370.377-0.1731-0.19760.29540.0034-0.01510.2031-0.06610.3537-25.024111.4638.487
710.63853.1741-4.98633.59481.40495.53570.1692-0.66770.34620.2266-0.01470.05210.1530.4782-0.15450.35610.0351-0.03830.2033-0.01940.2395-23.97119.86846.496
813.22060.97910.47388.1021-2.32522.4967-0.1433-0.25460.4773-0.02240.40260.1433-0.35510.069-0.25930.34630.02080.03260.2203-0.04460.2431-28.352124.49345.111
98.5577-4.30510.67826.69580.64085.41760.29490.16310.5586-0.6617-0.1381-0.0519-0.44360.1278-0.15680.3744-0.00940.0220.2050.03450.2732-28.987126.57435.776
105.5999-3.9993-1.66446.9147-3.55756.0947-0.23590.0645-0.4589-0.03550.36980.48290.3532-0.5211-0.13390.3534-0.0424-0.03530.1495-0.0690.3171-19.869108.46336.304
113.83360.9997-1.14970.8352-1.24972.0092-0.2392-0.3856-0.4351-0.06530.1896-0.05570.2901-0.37360.04960.50450.02110.04350.26860.02580.3434-23.32199.66767.146
126.01393.42011.37079.29530.20795.3872-0.0241-0.1186-0.25620.0916-0.16050.23560.2804-0.15670.18460.26730.02320.04740.2065-0.01370.2068-22.212101.04963.665
130.93542.9832-1.828714.96082.302517.80130.2958-0.2015-0.0360.7804-0.2183-0.2373-0.01090.1765-0.07750.6717-0.14240.02450.70020.01820.5503-17.218121.92766.489
144.407-1.1045-1.7694.0923-0.0973.4118-0.039-0.2782-0.20930.099-0.03250.07940.06450.29410.07140.2225-0.0255-0.08080.07180.0010.1428-8.04109.58455.284
151.34510.28820.13581.31010.71752.93770.0094-0.0118-0.0172-0.1408-0.0756-0.117-0.03890.28970.06620.30140.03040.00290.0532-0.00990.2476-6.29112.19248.642
161.6988-0.38292.62520.9458-1.8396.2841-0.09860.32580.2776-0.0537-0.15-0.0215-0.35940.41250.24860.4310.09030.02170.22270.0290.3086-12.647126.72832.695
170.90231.04860.52243.5497-1.03664.2327-0.04390.16610.1608-0.5106-0.1040.3718-0.2389-0.18570.1480.45380.0641-0.04230.21380.04790.2945-11.126123.58827.632
182.3230.16660.39522.3029-0.86362.4508-0.04960.33750.0124-0.3116-0.01150.0662-0.03790.2510.06110.46450.03730.0310.2288-0.0520.2108-7.463114.03329.008
1910.22514.7898-8.02934.84610.391113.4894-0.0459-0.2424-0.0446-0.41560.0096-0.1877-0.1960.57720.03630.45460.17030.0590.37920.03740.35726.657102.7835.197
201.51370.40480.02638.07650.92792.20680.19450.37310.1741-0.3186-0.1823-0.276-0.17520.3949-0.01230.3697-0.01120.02150.32670.01540.2208-2.384119.59427.251
2113.6713-1.51294.07552.7622-0.16372.9611-0.1167-0.30620.11430.36690.07920.2311-0.2328-0.28440.03760.4066-0.0329-0.00280.27330.02120.333418.191135.3482.494
221.7548-2.437-3.627920.973823.525427.06840.35410.3626-0.1384-0.40530.3709-1.0334-0.47510.3677-0.7250.72450.08150.05440.72960.27490.920632.269131.7463.495
238.0512-0.32192.65938.9023-3.743512.5586-0.23240.5530.84460.1104-0.0246-0.5514-0.6581-0.03290.25710.3347-0.03960.02130.16470.03030.397421.719136.965-1.224
241.6906-3.15041.8367.2328-1.66694.3160.0042-0.081-0.0716-0.11750.12530.1486-0.0286-0.1684-0.12950.30870.0146-0.00480.21410.03570.369311.115129.759-3.897
2511.84522.93632.27074.2603-7.420218.5-0.1810.2963-0.3231-0.25280.0847-0.14030.3782-0.04160.09630.33090.094-0.06530.28520.01430.354119.128126.55-6.397
266.50931.93845.011724.02683.60444.0692-0.25640.14970.2348-0.53440.2278-0.5687-0.23930.09350.02870.3270.03340.0420.32560.0970.502326.209131.091-6.453
272.03462.33483.36298.1624-1.89411.6742-0.23680.1241-0.2625-0.99290.3586-0.64320.4174-0.1447-0.12180.3520.00120.03190.28670.06730.471226.741122.728-3.057
285.62692.75496.97369.72726.839614.45190.214-0.2529-0.3127-0.0054-0.1710.0821-0.06260.0073-0.04290.24730.01440.04030.2390.05320.35115.816121.9524.691
298.4177-4.5084-2.79894.00822.79428.963-0.1588-0.2279-0.00850.16230.1420.50610.374-0.99260.01670.31470.01640.02350.19550.03290.451310.573125.8991.89
305.1971-5.3298-0.879210.49440.40460.59940.0330.28080.2380.2773-0.2549-0.0236-0.2649-0.01430.22190.35280.013-0.04860.23810.01990.273923.967125.8393.901
315.94350.9135-0.00283.53650.19466.8080.01540.5426-0.6788-0.5072-0.09870.22120.5757-0.08540.08320.41260.0028-0.07280.1191-0.07370.446910.79298.412-14.159
328.0826-0.7244-2.04284.5782-0.04848.8440.06840.1985-0.1779-0.2015-0.15730.02060.05710.17660.0890.37180.0022-0.11270.1279-0.01760.361212.627102.044-12.754
3315.9582-4.15392.94533.5132-0.64428.08110.0394-0.3178-0.394-0.2044-0.0350.24440.1246-0.5255-0.00430.3391-0.03830.01150.27990.00390.46560.536107.1046.436
343.1288-0.07280.07491.9955-0.07741.97730.04210.0748-0.17220.0225-0.00080.24980.26460.043-0.04140.2460.0026-0.0150.0050.01780.258721.728101.4387.344
353.5106-3.9346-0.570410.7915-1.28680.7343-0.0868-0.1918-0.28120.614-0.05930.1842-0.00170.05330.14620.4422-0.07920.07670.27340.03950.351415.412101.65116.626
362.22470.37440.30032.01811.27192.8376-0.0101-0.20270.143-0.0348-0.00690.2008-0.0046-0.03060.0170.2369-0.0145-0.0060.03270.05180.324320.978109.056.884
374.2083.9225-0.61996.6375-0.96922.8010.3851-0.19320.52850.2149-0.38330.4046-0.1154-0.146-0.00180.27170.10.03750.1449-0.03130.414925.792129.38321.369
381.23220.1538-0.44891.9835-0.05151.83870.1283-0.11950.36710.22870.06640.0199-0.10360.0735-0.19460.28470.02240.03120.0702-0.02270.30535.449121.64919.115
391.9553-0.99372.81864.0287-2.19557.72430.0877-0.0438-0.03650.0649-0.0702-0.03720.050.1623-0.01750.20560.01030.03150.1855-0.02370.241838.8103.21513.061
402.1449-1.0509-0.99162.73280.86234.9930.0172-0.24840.0880.26320.0185-0.0595-0.19930.1038-0.03570.3052-0.06690.02330.1292-0.02370.244235.573117.58623.562
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 84
2X-RAY DIFFRACTION2A85 - 90
3X-RAY DIFFRACTION3A91 - 95
4X-RAY DIFFRACTION4A96 - 107
5X-RAY DIFFRACTION5A108 - 114
6X-RAY DIFFRACTION6A115 - 124
7X-RAY DIFFRACTION7A125 - 134
8X-RAY DIFFRACTION8A135 - 140
9X-RAY DIFFRACTION9A141 - 147
10X-RAY DIFFRACTION10A148 - 154
11X-RAY DIFFRACTION11B1 - 45
12X-RAY DIFFRACTION12B46 - 62
13X-RAY DIFFRACTION13B63 - 69
14X-RAY DIFFRACTION14B70 - 107
15X-RAY DIFFRACTION15B108 - 169
16X-RAY DIFFRACTION16B170 - 195
17X-RAY DIFFRACTION17B196 - 224
18X-RAY DIFFRACTION18B225 - 279
19X-RAY DIFFRACTION19B280 - 296
20X-RAY DIFFRACTION20B297 - 316
21X-RAY DIFFRACTION21C79 - 85
22X-RAY DIFFRACTION22C86 - 90
23X-RAY DIFFRACTION23C91 - 95
24X-RAY DIFFRACTION24C96 - 102
25X-RAY DIFFRACTION25C103 - 108
26X-RAY DIFFRACTION26C109 - 113
27X-RAY DIFFRACTION27C114 - 123
28X-RAY DIFFRACTION28C124 - 132
29X-RAY DIFFRACTION29C133 - 140
30X-RAY DIFFRACTION30C141 - 154
31X-RAY DIFFRACTION31D4 - 43
32X-RAY DIFFRACTION32D44 - 62
33X-RAY DIFFRACTION33D63 - 72
34X-RAY DIFFRACTION34D73 - 126
35X-RAY DIFFRACTION35D127 - 144
36X-RAY DIFFRACTION36D145 - 178
37X-RAY DIFFRACTION37D179 - 209
38X-RAY DIFFRACTION38D210 - 267
39X-RAY DIFFRACTION39D268 - 295
40X-RAY DIFFRACTION40D296 - 316

+
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