[English] 日本語
Yorodumi
- PDB-7k1o: Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k1o
TitleCrystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-3',5'-Diphosphate
ComponentsUridylate-specific endoribonuclease
KeywordsVIRAL PROTEIN / SARS Corona virus 2 / endoribonuclease / COVID-19 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / 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
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 / : ...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 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
Chem-VQV / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKim, Y. / Maltseva, N. / Jedrzejczak, R. / Endres, M. / Welk, L. / Chang, C. / Michalska, K. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-3',5'-Diphosphate
Authors: Kim, Y. / Maltseva, N. / Jedrzejczak, R. / Endres, M. / Welk, L. / Chang, C. / Michalska, K. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
C: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3709
Polymers124,9723
Non-polymers1,3996
Water84747
1
A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
C: Uridylate-specific endoribonuclease
hetero molecules

A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
C: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,74118
Polymers249,9436
Non-polymers2,79712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area19630 Å2
ΔGint-98 kcal/mol
Surface area84480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.460, 151.321, 197.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Uridylate-specific endoribonuclease / NSP15 endoribnuclease


Mass: 41657.238 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: P0DTD1, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-VQV / 1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione


Mass: 404.161 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 8 % w/v Polyethylene glycol 4,000, 100 mM Sodium acetate; pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→49.68 Å / Num. obs: 49708 / % possible obs: 96.8 % / Redundancy: 7 % / Biso Wilson estimate: 60.63 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.144 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.497 / Mean I/σ(I) obs: 0.76 / Num. unique obs: 2066 / CC1/2: 0.463 / % possible all: 81.1

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 6VWW

6vww


Resolution: 2.4→49.68 Å / SU ML: 0.3736 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7132
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2425 2485 5.05 %
Rwork0.2068 46765 -
obs0.2086 49250 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.94 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8221 0 87 47 8355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318511
X-RAY DIFFRACTIONf_angle_d0.594711555
X-RAY DIFFRACTIONf_chiral_restr0.04591322
X-RAY DIFFRACTIONf_plane_restr0.00321472
X-RAY DIFFRACTIONf_dihedral_angle_d20.37973120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.34861250.34041918X-RAY DIFFRACTION72.24
2.45-2.50.38381260.33132215X-RAY DIFFRACTION82.26
2.5-2.550.34241040.32212315X-RAY DIFFRACTION86.67
2.55-2.610.35471360.3152426X-RAY DIFFRACTION90.31
2.61-2.680.32591340.31562528X-RAY DIFFRACTION93.73
2.68-2.750.33321890.29742560X-RAY DIFFRACTION97.03
2.75-2.830.32781210.29062715X-RAY DIFFRACTION99.58
2.83-2.920.29191300.26362724X-RAY DIFFRACTION99.86
2.92-3.020.32961340.27492675X-RAY DIFFRACTION99.89
3.02-3.150.3171740.26742665X-RAY DIFFRACTION99.89
3.15-3.290.29591020.25132750X-RAY DIFFRACTION99.96
3.29-3.460.27931510.24152716X-RAY DIFFRACTION99.97
3.46-3.680.27071370.21982707X-RAY DIFFRACTION99.82
3.68-3.960.23541280.2062743X-RAY DIFFRACTION100
3.96-4.360.26121440.17652746X-RAY DIFFRACTION99.83
4.36-4.990.2031240.15022737X-RAY DIFFRACTION100
4.99-6.290.18661530.17212784X-RAY DIFFRACTION99.83
6.29-49.680.17791730.16022841X-RAY DIFFRACTION99.28
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)
12.933619181010.37795138558-0.3901857646053.716679297260.3269279636882.869181985630.118737478178-0.1078422895390.3984718534310.3947813806710.1105427146330.124527874197-0.201449158535-0.686845531065-0.2497529267920.4341209219680.03712185498990.01024542552130.5654946784920.08372875912640.56805010102427.55507707747.7873404955-43.8656195359
22.309487263540.900357081731-0.9839549846231.00381668034-0.1766231064991.94204016545-0.1650090150070.6598279875030.209705203488-0.1960755310010.2923698431010.1904163400540.387435449604-1.09697843621-0.1407207314160.455315669252-0.206293413468-0.02121102079450.9695696163070.08608031346650.5743711388511.830060301629.8992179623-37.8305180347
31.8436600441-0.4450491397942.973830743271.19456536478-0.1891920304034.91427109248-0.7861920654440.7600340664510.198496783387-0.1415953577170.6500318001440.3414075328350.01201979576-0.1373055772330.1233408445130.634233061533-0.3475430717370.06373545554450.9894320328550.01660211853570.7066768805214.727401809520.5715293573-26.7046977027
43.90995211952-0.6245382626360.6758407316451.72925003624-0.4229242073241.57613457082-0.00283272535037-0.263469531609-0.3344269583040.1246270519660.1178201720680.2609922877940.883551295456-0.289928475846-0.1080097003520.911801752125-0.1362793541560.01564209619540.4882709489140.05099922700060.47180751896828.26212307413.7916674496-16.6321155029
52.11840954079-0.2241154462810.395996393610.9582291378160.534444169393.8173636879-0.1228954533890.00815434733861-0.0120597703470.08783694850010.1676258122850.0362634894430.718495299987-0.137383668519-0.05561460909190.604925156147-0.129239772896-0.01053236619270.3776332191230.01613750460930.44798688349240.157986289721.2834040908-61.8759134062
62.37009004307-0.01663654395660.1477916922220.1051445492480.3790516077771.39899238093-0.0167889090478-0.138736684599-0.189970915560.1674742675420.02567108120690.1600455543571.05073689945-0.453388658338-0.08074805489451.0015942625-0.455974766181-0.001312941995280.735270253120.02376338811650.63425971748423.290580476214.8087884312-71.4857666969
71.525335390990.2354339862310.3469607022072.6538795090.628500372311.803578970770.06664186980140.1499154730450.050484212203-0.2588923373290.00492673938595-0.0354034270286-0.060955253319-0.591166827366-0.1041306777190.462257870327-0.0958291943671-0.04147620778380.7533596552550.09991206237390.53883587002428.50175463241.0401546232-88.8585352469
81.09184459597-1.063928635230.1613603801713.45107516932-0.2219451623811.613054925010.2481679735660.2450822153980.230781882710.4932734943690.3079227960981.1200489955-0.161625770962-1.07186747604-0.3943023152560.655355364698-0.03569924753470.02622752615241.304830219220.2650532519660.84025533295513.69841581442.4845747649-86.1090739807
93.05939136605-0.6750200628410.2005289798562.921040071061.835041400534.502039600070.00403756779153-0.0303047009247-0.1341926357410.3898613664480.224048168975-0.2738525090280.04890649118791.13703508571-0.1653347393270.4254232651180.01327165983750.004868189973080.656038456437-0.06802584875530.59447504675260.314582258145.848035463-38.1592892932
102.93691794157-0.381212635232-0.5893281273772.07927882524-0.05143333746752.95822353075-0.1050107644690.1221935244650.4008423512580.1938030191820.273258268224-0.04089949925170.2763212192260.0254301844426-0.1677572147050.520396489934-0.02131352331-0.001395458525450.456347598915-0.09785061121760.61377029081651.42901207746.9075034678-39.1694611246
111.01999923021-0.533969979457-0.08060848068130.696462100323-0.7150204787091.928656910250.144631306408-0.05597454471450.423901534887-0.439411338859-0.01019214124140.0625526535172-0.7507401497070.31922101487-0.1086839993560.840414314094-0.09919169121130.1118676581280.412752962028-0.07369753063480.72071605702648.298467872464.5276271408-35.4106507026
121.1240957862-0.1071385873890.4368804227751.103095250210.8214272328880.8045590763840.210646393275-0.102230394250.6314144230390.3881738407840.101558073413-0.130410535764-0.9278660362590.60212759626-0.1971805448361.03102960212-0.06161987688610.1342212267120.376017973353-0.127925917280.85171050200847.796627671476.5626472038-26.4434015679
130.603023966803-0.286128730131-0.09467545237191.18314478433-0.1326198766360.939236687650.210291440728-0.2595941254490.275509067310.3319715979140.1996095343110.560856750768-0.4534864155980.311685082141-0.432534534340.844763155233-0.08709647068630.1002123277990.473003831858-0.05989579662150.78587729891545.922605206665.8816070727-21.058648133
142.479143802822.45932655067-0.8331432762872.52098660914-1.395568612152.542739033070.210396233719-0.146892230360.302400648414-0.84301864157-0.367515283109-0.483494152567-0.323161700876-0.2300820017250.02774213322410.8329433230350.1345566657240.1953769603680.577339409666-0.06807307180420.77583772006535.596846555867.9754060475-22.3073764389
151.70494772871-0.3775729062050.1007574348071.79419979328-0.2606371707491.570163257490.4144377911-1.24658579050.7293134575910.605623045226-0.2229100410730.393213726541-0.323293081935-0.851571988115-0.2428555268520.9014845941330.02045391099520.1980032503231.02877666629-0.1927839029760.87984390040821.150259335358.5756910066-6.9021365628
162.807361874891.30237703137-0.1875811569221.859244970010.1972727470761.378172035340.523305997768-0.3893085426520.0610947258774-0.209360464541-0.381925669290.0362581723952-0.286154270144-0.737910526456-0.1966415737510.7338676645890.1016352426810.1642670673960.6932383776150.02042152908870.72823082629520.483561409948.7525425926-17.8764256634
172.320281984970.0929958368364-0.2083029243222.376563736441.220720100141.67736938713-0.0827981668827-0.4557523852490.477896124482-0.07204236742140.05897738157270.178650906028-0.366363144395-0.3841721438830.01822831546390.6893506308690.1076300923830.09695750320280.652150869887-0.0537541775080.72000621221124.020392807855.7433337413-22.6800124707
181.096238946070.423666227463-0.2422171835911.92909100892-0.4935080117321.399507433530.177432034265-0.3020619771581.27168979290.1487699445040.2813271995581.16508525042-0.47839471064-0.750965734945-0.5097721911110.8941071274050.3137190872080.154239987510.8259264527310.02042245457251.2614612083316.704488552867.5977762429-23.4075663363
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 60 )AA1 - 601 - 60
22chain 'A' and (resid 61 through 183 )AA61 - 18361 - 183
33chain 'A' and (resid 184 through 203 )AA184 - 203184 - 203
44chain 'A' and (resid 204 through 346 )AA204 - 346204 - 346
55chain 'B' and (resid 0 through 95 )BD0 - 951 - 96
66chain 'B' and (resid 96 through 187 )BD96 - 18797 - 188
77chain 'B' and (resid 188 through 309 )BD188 - 309189 - 310
88chain 'B' and (resid 310 through 346 )BD310 - 346311 - 347
99chain 'C' and (resid 0 through 38 )CG0 - 381 - 43
1010chain 'C' and (resid 39 through 60 )CG39 - 6044 - 65
1111chain 'C' and (resid 61 through 130 )CG61 - 13066 - 135
1212chain 'C' and (resid 131 through 160 )CG131 - 160136 - 165
1313chain 'C' and (resid 161 through 183 )CG161 - 183166 - 188
1414chain 'C' and (resid 184 through 203 )CG184 - 203189 - 208
1515chain 'C' and (resid 204 through 236 )CG204 - 236209 - 241
1616chain 'C' and (resid 237 through 267 )CG237 - 267242 - 272
1717chain 'C' and (resid 268 through 309 )CG268 - 309273 - 314
1818chain 'C' and (resid 310 through 346 )CG310 - 346315 - 351

+
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