[English] 日本語
Yorodumi
- PDB-6xdh: Crystal Structure of NendoU (Uridylate-specific endoribonuclease,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xdh
TitleCrystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2
ComponentsUridylate-specific endoribonuclease
KeywordsHydrolase/VIRAL PROTEIN / SSGCID / endoribonuclease / nsp15 / COVID-19 / SARS-CoV-2 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / VIRAL PROTEIN / Hydrolase-VIRAL PROTEIN complex
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / 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 / host cell endoplasmic reticulum membrane / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface 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 / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / : / Coronavirus replicase NSP7
Similarity search - Domain/homology
ACETATE ION / CITRIC ACID / FORMIC ACID / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJun 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.2Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,64713
Polymers82,7942
Non-polymers85411
Water7,584421
1
A: Uridylate-specific endoribonuclease
hetero molecules

A: Uridylate-specific endoribonuclease
hetero molecules

A: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,22015
Polymers124,1913
Non-polymers1,03012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9790 Å2
ΔGint-47 kcal/mol
Surface area43430 Å2
MethodPISA
2
B: Uridylate-specific endoribonuclease
hetero molecules

B: Uridylate-specific endoribonuclease
hetero molecules

B: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,72224
Polymers124,1913
Non-polymers1,53121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area10700 Å2
ΔGint-36 kcal/mol
Surface area43880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.820, 150.820, 112.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Uridylate-specific endoribonuclease / NendoU / nsp15


Mass: 41396.930 Da / Num. of mol.: 2 / Fragment: BewuA.18928.a.MX151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Plasmid: BewuA.18928.a.MX151 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, Hydrolases; Acting on ester bonds

-
Non-polymers , 5 types, 432 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.45 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BewuA.18928.a.MX151.PW38806 at 36 mg/ml mixed 1:1 with Morpheus(G3): 10% (w/v) PEG 4000, 20% (v/v) glycerol, 0.1 M MES/imidazole, pH=6.5, 0.02 M of each sodium formate, ammonium acetate, ...Details: BewuA.18928.a.MX151.PW38806 at 36 mg/ml mixed 1:1 with Morpheus(G3): 10% (w/v) PEG 4000, 20% (v/v) glycerol, 0.1 M MES/imidazole, pH=6.5, 0.02 M of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium l-tartrate, sodium oxamate. Tray: 315968g8, puck: teq6-3.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 24, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 60593 / % possible obs: 100 % / Redundancy: 11.456 % / Biso Wilson estimate: 46.957 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.081 / Χ2: 0.923 / Net I/σ(I): 22.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.4111.4860.5944.1544540.950.621100
2.41-2.4811.50.4825.0443680.9680.504100
2.48-2.5511.5170.4115.9341960.9760.43100
2.55-2.6311.5110.3516.9441120.9790.367100
2.63-2.7111.5220.2798.6339970.9870.292100
2.71-2.8111.5240.20911.4338720.9920.219100
2.81-2.9111.530.17113.936990.9940.179100
2.91-3.0311.5370.14116.5335990.9960.147100
3.03-3.1711.5160.1120.6934190.9980.115100
3.17-3.3211.5090.08825.1832910.9980.092100
3.32-3.511.4710.0731.2231500.9980.074100
3.5-3.7211.4470.06135.729540.9990.064100
3.72-3.9711.4260.05539.127950.9990.058100
3.97-4.2911.4040.04844.8225960.9990.05100
4.29-4.711.410.04447.9323980.9990.046100
4.7-5.2511.4020.04249.2821660.9990.043100
5.25-6.0711.4130.04347.1919260.9990.045100
6.07-7.4311.3210.04148.6616210.9990.043100
7.43-10.5111.0950.03855.4812730.9990.039100
10.51-509.9280.03954.997070.9990.04198.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6vww

6vww


Resolution: 2.35→45.21 Å / SU ML: 0.1908 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.2715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1825 2078 3.43 %
Rwork0.1572 58473 -
obs0.1581 60551 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.51 Å2
Refinement stepCycle: LAST / Resolution: 2.35→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 57 421 5928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00665663
X-RAY DIFFRACTIONf_angle_d0.80127694
X-RAY DIFFRACTIONf_chiral_restr0.0547883
X-RAY DIFFRACTIONf_plane_restr0.0047995
X-RAY DIFFRACTIONf_dihedral_angle_d19.42442055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.25121130.19413879X-RAY DIFFRACTION99.97
2.4-2.460.21181390.19093899X-RAY DIFFRACTION100
2.46-2.530.23881390.18653859X-RAY DIFFRACTION99.93
2.53-2.610.20911320.19033925X-RAY DIFFRACTION99.98
2.61-2.690.22371450.19013866X-RAY DIFFRACTION100
2.69-2.790.2041400.18043855X-RAY DIFFRACTION99.97
2.79-2.90.23791470.18053920X-RAY DIFFRACTION100
2.9-3.030.23691440.18333870X-RAY DIFFRACTION99.98
3.03-3.190.21551150.17623925X-RAY DIFFRACTION99.98
3.19-3.390.19171300.16813892X-RAY DIFFRACTION100
3.39-3.650.17751510.15613874X-RAY DIFFRACTION100
3.65-4.020.16661300.1443934X-RAY DIFFRACTION100
4.02-4.60.14581460.12813903X-RAY DIFFRACTION100
4.6-5.790.13571430.13363909X-RAY DIFFRACTION99.98
5.79-45.210.1741640.14673963X-RAY DIFFRACTION99.73
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)
16.58855622364-0.03488861808031.915421873717.503654419191.369118839985.438565055350.2339938929950.302865117678-0.6048768504430.2047278495770.0295479741779-0.4518937088380.6586120855360.141166320865-0.2164811499410.3360905763480.0330690256118-0.02416853672940.302801742058-0.03890528560120.265038821213-3.095661173466.321489411148.287738331
23.1371259890.2485486433111.113030910681.8695348694-0.1651764411361.92224263364-0.02428522720940.213986199831-0.131042586534-0.1757729955080.07401451026030.3240974681420.160810769895-0.147831121366-0.03940925158350.269217449282-0.0453343279236-0.0329053577120.269826320178-0.04237028991810.276959849384-23.68357129673.547113507340.3072088963
31.686159292130.413977392397-0.2339621095073.28273172004-0.5898085318611.20761785076-0.1623059776890.7547875286530.16116728431-1.023597255340.2270308324480.32112685648-0.121473349248-0.161723375461-0.05117372123830.713642173101-0.104338582674-0.151256096260.6431946514030.0810989570580.361105863847-21.215750682395.566317575821.2252942653
45.00724670496-1.46151510048-0.6461539101477.76929355035-2.788519670784.14799960790.3586777198060.4333459884220.952435713904-0.2187093817790.1559501595841.47937581165-0.740296183454-0.337978817191-0.4121985565890.6152684656150.00637016034942-0.1878187193830.5856665407430.1554533736750.828167223616-33.7681669419101.68899449825.4936079599
55.766113523530.4795693583911.393926985528.282467185140.04645311882885.404789047630.1142977008660.0311792239784-0.4659403410750.04532410914170.0112425551352-0.06494429203110.4724412994970.274169051506-0.1522320887050.3220196226380.00533486620068-0.027493746760.233944789867-0.02328320575990.199145659386-62.551827017626.86075088137.8986912597
61.860295678750.671722473180.7939527031143.082312402991.471366282992.755678932440.1086343371670.0822690931799-0.0875547967156-0.0271959514090.270628385766-0.8977263023240.05879652456320.538736356132-0.2348789285320.224077624610.00614182445888-0.008687025709280.323218602504-0.06261024628560.512789754436-48.587186701442.643281918215.7771504856
73.711464453130.0963061724658-1.172651429543.092029012991.176532917663.58293309532-0.0459978209106-0.437042635237-0.2040651621450.4720779311810.126425204637-0.4919286312160.106152680610.178368048182-0.1673789517890.349679116874-0.0434824445834-0.1486180770060.387740932758-0.002791779387480.441164345047-52.019894427655.978202981935.56205825
83.14910161241-0.778463964116-0.4537154117022.480233207150.58408045441.71267914130.123558391579-0.3541995997920.3860762686760.306941048349-0.110843285604-0.113725837076-0.0924098122672-0.0591262648919-0.02920892419810.292230332157-0.0675984676359-0.01539500381230.36302871915-0.08785988883790.32566350246-62.075699619964.544854305232.8787908794
95.03202910811-4.15222547751-2.733710072824.184308541551.237208988673.112621394390.5824278520930.1975201522131.03944246996-0.11320952136-0.109125277002-0.371011472605-0.300667262944-0.633240779622-0.3936411917620.389975651237-0.0750464678954-0.008001794396350.503489146172-0.08680698851680.590080898473-56.094859156273.050499547530.1561293782
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 38 )AA0 - 381 - 43
22chain 'A' and (resid 39 through 183 )AA39 - 18344 - 190
33chain 'A' and (resid 184 through 309 )AA184 - 309191 - 316
44chain 'A' and (resid 310 through 346 )AA310 - 346317 - 353
55chain 'B' and (resid -1 through 38 )BF-1 - 381 - 42
66chain 'B' and (resid 39 through 177 )BF39 - 17743 - 187
77chain 'B' and (resid 178 through 225 )BF178 - 225188 - 235
88chain 'B' and (resid 226 through 325 )BF226 - 325236 - 337
99chain 'B' and (resid 326 through 347 )BF326 - 347338 - 359

+
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