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- PDB-7tj2: SARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA -

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Basic information

Entry
Database: PDB / ID: 7tj2
TitleSARS-CoV-2 endoribonuclease Nsp15 bound to dsRNA
Components
  • (RNA (31-MER)) x 2
  • Uridylate-specific endoribonuclease nsp15
KeywordsVIRAL PROTEIN/RNA / endoribonuclease / VIRAL PROTEIN / VIRAL PROTEIN-RNA 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) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...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 / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / 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 / double membrane vesicle viral factory outer membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease 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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / SARS-CoV-2 modulates host translation machinery / 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 / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / 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
Nsp15 N-terminal domain-like / nsp15 middle domain / Double Stranded RNA Binding Domain / 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. ...Nsp15 N-terminal domain-like / nsp15 middle domain / Double Stranded RNA Binding Domain / 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 / Betacoronavirus single-stranded poly(A) binding domain / 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 / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus replicase NSP1 / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / 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
RNA / RNA (> 10) / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFrazier, M.N. / Krahn, J.M. / Butay, K.J. / Dillard, L.B. / Borgnia, M.J. / Stanley, R.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA ES103247 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC ES103326 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1ZIAES103340 United States
Citation
Journal: Nucleic Acids Res / Year: 2022
Title: Flipped over U: structural basis for dsRNA cleavage by the SARS-CoV-2 endoribonuclease.
Authors: Meredith N Frazier / Isha M Wilson / Juno M Krahn / Kevin John Butay / Lucas B Dillard / Mario J Borgnia / Robin E Stanley
Abstract: Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, ...Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is a uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.
#1: Journal: bioRxiv / Year: 2022
Title: Flipped Over U: Structural Basis for dsRNA Cleavage by the SARS-CoV-2 Endoribonuclease.
Authors: Meredith N Frazier / Isha M Wilson / Juno M Krahn / Kevin John Butay / Lucas B Dillard / Mario J Borgnia / Robin E Stanley /
Abstract: Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, ...Coronaviruses generate double-stranded (ds) RNA intermediates during viral replication that can activate host immune sensors. To evade activation of the host pattern recognition receptor MDA5, coronaviruses employ Nsp15, which is uridine-specific endoribonuclease. Nsp15 is proposed to associate with the coronavirus replication-transcription complex within double-membrane vesicles to cleave these dsRNA intermediates. How Nsp15 recognizes and processes dsRNA is poorly understood because previous structural studies of Nsp15 have been limited to small single-stranded (ss) RNA substrates. Here we present cryo-EM structures of SARS-CoV-2 Nsp15 bound to a 52nt dsRNA. We observed that the Nsp15 hexamer forms a platform for engaging dsRNA across multiple protomers. The structures, along with site-directed mutagenesis and RNA cleavage assays revealed critical insight into dsRNA recognition and processing. To process dsRNA Nsp15 utilizes a base-flipping mechanism to properly orient the uridine within the active site for cleavage. Our findings show that Nsp15 is a distinctive endoribonuclease that can cleave both ss- and dsRNA effectively.
History
DepositionJan 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uridylate-specific endoribonuclease nsp15
B: Uridylate-specific endoribonuclease nsp15
C: Uridylate-specific endoribonuclease nsp15
D: Uridylate-specific endoribonuclease nsp15
E: Uridylate-specific endoribonuclease nsp15
F: Uridylate-specific endoribonuclease nsp15
G: RNA (31-MER)
H: RNA (31-MER)


Theoretical massNumber of molelcules
Total (without water)268,7908
Polymers268,7908
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "C" and (resid 0 or (resid 1 and (name...
d_2ens_1(chain "B" and resid 0 through 47)
d_3ens_1(chain "A" and resid 0 through 47)
d_4ens_1(chain "D" and resid 0 through 47)
d_5ens_1(chain "E" and resid 0 through 47)
d_6ens_1(chain "F" and resid 0 through 47)
d_1ens_2(chain "C" and resid 50 through 188)
d_2ens_2(chain "B" and resid 50 through 188)
d_3ens_2(chain "A" and resid 50 through 188)
d_4ens_2(chain "D" and resid 50 through 188)
d_5ens_2(chain "E" and resid 50 through 188)
d_6ens_2(chain "F" and resid 50 through 188)
d_1ens_3(chain "A" and (resid 195 through 206 or resid 249 through 299))
d_2ens_3(chain "B" and (resid 195 through 206 or resid 249 through 299))
d_3ens_3(chain "C" and (resid 195 through 206 or resid 249 through 299))
d_4ens_3(chain "D" and resid 195 through 299)
d_5ens_3(chain "E" and (resid 195 through 206 or resid 249 through 299))
d_6ens_3(chain "F" and (resid 195 through 206 or resid 249 through 299))
d_1ens_4(chain "B" and (resid 314 through 334 or resid 341 through 345))
d_2ens_4(chain "C" and (resid 314 through 334 or resid 341 through 345))
d_3ens_4(chain "E" and (resid 314 through 334 or resid 341 through 345))
d_4ens_4(chain "F" and (resid 314 through 334 or resid 341 through 345))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLULYSC2 - 49
d_21ens_1GLULYSB2 - 49
d_31ens_1GLULYSA2 - 49
d_41ens_1GLULYSD2 - 49
d_51ens_1GLULYSE2 - 49
d_61ens_1GLULYSF2 - 49
d_11ens_2LEUGLNC52 - 190
d_21ens_2LEUGLNB52 - 190
d_31ens_2LEUGLNA52 - 190
d_41ens_2LEUGLND52 - 190
d_51ens_2LEUGLNE52 - 190
d_61ens_2LEUGLNF52 - 190
d_11ens_3PHEPROA197 - 208
d_12ens_3LEULEUA251 - 301
d_21ens_3PHEPROB197 - 208
d_22ens_3LEULEUB251 - 301
d_31ens_3PHEPROC197 - 208
d_32ens_3LEULEUC251 - 301
d_41ens_3PHELEUD197 - 259
d_51ens_3PHEPROE197 - 208
d_52ens_3LEULEUE251 - 301
d_61ens_3PHEPROF197 - 208
d_62ens_3LEULEUF251 - 301
d_11ens_4VALCYSB316 - 336
d_12ens_4THRLYSB343 - 347
d_21ens_4VALCYSC316 - 336
d_22ens_4THRLYSC343 - 347
d_31ens_4VALCYSE316 - 336
d_32ens_4THRLYSE343 - 347
d_41ens_4VALCYSF316 - 336
d_42ens_4THRLYSF343 - 347

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

NCS oper:
IDCodeMatrixVector
1given(-0.45149147147, -0.87348987978, -0.182128748724), (0.830613911613, -0.486003937748, 0.271810048248), (-0.325938615424, -0.0285587537509, 0.944959478792)300.555212585, 54.2275886359, 48.3671155526
2given(-0.460959827356, 0.826621670707, -0.322819843073), (-0.870003191972, -0.492670044069, -0.0192528863949), (-0.174958519431, 0.271979486717, 0.946264590526)107.537062572, 289.684084037, -6.82935369216
3given(0.330694474661, 0.930774218974, 0.155886233268), (0.932770750628, -0.34747053506, 0.0959320282164), (0.14345693152, 0.113681927144, -0.983105552949)-52.5079653968, 44.54917187, 188.207488687
4given(-0.989117311799, -0.145258079507, 0.0233887544913), (-0.147038849427, 0.970376954654, -0.191698050684), (0.00514978233118, -0.19305091612, -0.9811752257)251.923241058, 42.3050556955, 242.264947649
5given(0.571599128168, -0.748364771507, 0.336488640885), (-0.74703601192, -0.644268330551, -0.163876524074), (0.339428392407, -0.157697454055, -0.927318650418)105.804835134, 309.603399816, 192.168969573
6given(-0.461444336885, -0.869749061967, -0.174944828914), (0.825474081215, -0.493175676623, 0.274536506187), (-0.325056403103, -0.0177291058625, 0.945528430882)300.418149322, 55.2787799224, 46.9341560261
7given(-0.448697602298, 0.832423146911, -0.325180205699), (-0.875987770688, -0.481715292259, -0.0244090722876), (-0.176962954592, 0.273901591252, 0.945336993358)105.922775969, 289.888557243, -6.75559331331
8given(0.323603361261, 0.933830482688, 0.1524516126), (0.93302580994, -0.341716837134, 0.112660734975), (0.157301311395, 0.105783896803, -0.981868659552)-51.5879685365, 41.6637950433, 187.177688094
9given(-0.989041598602, -0.147596836512, 0.00344820050502), (-0.145250733773, 0.968607133686, -0.201748469415), (0.0264374842492, -0.200038482359, -0.979431296724)254.598957054, 43.6901610321, 240.164783234
10given(0.571085186312, -0.747592431329, 0.33906823295), (-0.746364101659, -0.644840148714, -0.164687007264), (0.341763569928, -0.15901804686, -0.926234809885)105.47522708, 309.664543566, 191.941686781
11given(-0.458584967506, 0.828350613947, -0.321768687027), (-0.87077093027, -0.491134750166, -0.0233376129215), (-0.177363509706, 0.269484540471, 0.946530648142)106.990833615, 290.291345359, -6.31902528409
12given(-0.455505258748, -0.873843820956, -0.170035101757), (0.828353170939, -0.48600693319, 0.278618529691), (-0.326107318914, -0.0139369102527, 0.94523001385)299.712892342, 53.4343655231, 46.8843107609
13given(0.581385741976, -0.739139564564, 0.340093109491), (-0.740021005843, -0.654110865601, -0.156549948619), (0.338170859089, -0.160660136931, -0.92726953496)103.141183735, 309.219212966, 192.504951576
14given(0.327933157677, 0.936932934788, 0.120898799848), (0.934363137004, -0.340558316062, 0.104812029699), (0.139374934277, 0.0785920420243, -0.98711596007)-48.5478364934, 42.19520986, 192.758584061
15given(-0.988840961568, -0.148475493912, 0.0121893573336), (-0.147718528852, 0.966608919841, -0.209395397077), (0.0193077434781, -0.208859339727, -0.977755075288)253.759146612, 45.0152683665, 241.83136288
16given(-0.449536595511, 0.834323185344, -0.319095082529), (-0.882083766444, -0.470957624655, 0.0112758483486), (-0.140872560395, 0.286537498729, 0.947655624977)104.744149755, 283.398144323, -12.3786568875
17given(0.575168522279, -0.745538181632, 0.336680843987), (-0.750382000572, -0.644732064051, -0.145764943669), (0.325742266519, -0.168799838015, -0.930268020782)104.756292486, 307.499038363, 195.520404301
18given(0.337687474201, 0.929197972893, 0.150194197424), (0.928520947526, -0.355011523299, 0.108699900326), (0.154324397855, 0.102751863718, -0.982662726844)-52.0985463815, 44.4227185606, 188.411101275

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Components

#1: Protein
Uridylate-specific endoribonuclease nsp15 / NendoU / Non-structural protein 15 / nsp15


Mass: 39246.684 Da / Num. of mol.: 6 / Mutation: H235A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0DTD1, Lyases; Phosphorus-oxygen lyases
#2: RNA chain RNA (31-MER)


Mass: 16781.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (31-MER)


Mass: 16528.768 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structural Basis for dsRNA cleavage by the SARS-CoV-2 Endoribonuclease
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.250 MDa / Experimental value: NO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: -1200 nm / Nominal defocus min: 2200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20_4459refinement
PHENIX1.20_4459refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 396312 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 65.86 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001717556
ELECTRON MICROSCOPYf_angle_d0.3724111
ELECTRON MICROSCOPYf_chiral_restr0.04052824
ELECTRON MICROSCOPYf_plane_restr0.00292873
ELECTRON MICROSCOPYf_dihedral_angle_d8.29756555
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CELECTRON MICROSCOPYNCS constraints7.92120752241E-13
ens_1d_3CELECTRON MICROSCOPYNCS constraints1.28611694809E-10
ens_1d_4CELECTRON MICROSCOPYNCS constraints6.36512965017E-13
ens_1d_5CELECTRON MICROSCOPYNCS constraints1.45951644508E-11
ens_1d_6CELECTRON MICROSCOPYNCS constraints1.17273933076E-13
ens_2d_2CELECTRON MICROSCOPYNCS constraints6.14190293656E-13
ens_2d_3CELECTRON MICROSCOPYNCS constraints7.14321987524E-12
ens_2d_4CELECTRON MICROSCOPYNCS constraints5.81989938182E-13
ens_2d_5CELECTRON MICROSCOPYNCS constraints1.57007586849E-13
ens_2d_6CELECTRON MICROSCOPYNCS constraints1.27904376578E-13
ens_3d_2AELECTRON MICROSCOPYNCS constraints1.43554687961E-11
ens_3d_3AELECTRON MICROSCOPYNCS constraints2.55132225767E-12
ens_3d_4AELECTRON MICROSCOPYNCS constraints1.36424263776E-13
ens_3d_5AELECTRON MICROSCOPYNCS constraints1.00484924407E-13
ens_3d_6AELECTRON MICROSCOPYNCS constraints1.26281393919E-12
ens_4d_2BELECTRON MICROSCOPYNCS constraints1.48113857705E-11
ens_4d_3BELECTRON MICROSCOPYNCS constraints8.42019887778E-11
ens_4d_4BELECTRON MICROSCOPYNCS constraints4.73066128445E-11

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