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- PDB-6x4i: Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in th... -

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Basic information

Entry
Database: PDB / ID: 6x4i
TitleCrystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with 3'-uridinemonophosphate
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 / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / mRNA guanylyltransferase activity / 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 / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / mRNA guanylyltransferase activity / 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 / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / 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 / symbiont-mediated suppression of host NF-kappaB cascade / host cell Golgi apparatus / DNA helicase / symbiont-mediated perturbation of host ubiquitin-like protein modification / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lyase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / copper ion binding / symbiont-mediated suppression of host gene expression / symbiont-mediated activation of host autophagy / viral translational frameshifting / 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
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 / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus ...Nsp15 N-terminal domain-like / nsp15 middle domain / Double Stranded RNA Binding Domain / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) profile. / 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 / Betacoronavirus replicase NSP1 / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / : / Coronavirus replicase NSP2, N-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
Similarity search - Domain/homology
3'-URIDINEMONOPHOSPHATE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChang, C. / Kim, Y. / Maltseva, N. / Jedrzejczak, R. / Endres, M. / 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
Citation
Journal: Commun Biol / Year: 2021
Title: Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.
Authors: Kim, Y. / Wower, J. / Maltseva, N. / Chang, C. / Jedrzejczak, R. / Wilamowski, M. / Kang, S. / Nicolaescu, V. / Randall, G. / Michalska, K. / Joachimiak, A.
#1: Journal: Biorxiv / Year: 2020
Title: Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Authors: Kim, Y. / Wower, J. / Maltseva, N. / Chang, C. / Jedrzejczak, R. / Wilamowski, M. / Kang, S. / Nicolaescu,, N. / Randall, G. / Michalska, K. / Joachimiak, A. / Center for Structural Genomics ...Authors: Kim, Y. / Wower, J. / Maltseva, N. / Chang, C. / Jedrzejczak, R. / Wilamowski, M. / Kang, S. / Nicolaescu,, N. / Randall, G. / Michalska, K. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 2.0Jun 10, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Revision 2.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,22725
Polymers83,3142
Non-polymers1,91323
Water12,935718
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A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)255,68275
Polymers249,9436
Non-polymers5,73869
Water1086
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 area32560 Å2
ΔGint-4 kcal/mol
Surface area82870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.940, 150.940, 111.858
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Uridylate-specific endoribonuclease / NSP15 endoribnuclease


Mass: 41657.238 Da / Num. of mol.: 2
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 BL21(DE3) (bacteria)
References: UniProt: P0DTD1, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-U3P / 3'-URIDINEMONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.41 Å3/Da / Density % sol: 72.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2M Sodium Chloride, 0.1M Sodium Potassium phosphate, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 122922 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.041 / Rrim(I) all: 0.152 / Χ2: 1.005 / Net I/σ(I): 6.3 / Num. measured all: 1578786
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.886.41.58761200.5610.6481.720.90799.7
1.88-1.928.51.49561110.7070.521.5860.905100
1.92-1.9510.81.36261030.820.4221.4270.915100
1.95-1.9911.71.18661120.8570.3551.2390.92100
1.99-2.0412.31.0261580.910.2981.0630.936100
2.04-2.0812.80.89360930.9340.2560.9290.939100
2.08-2.1413.10.83261540.9470.2350.8650.935100
2.14-2.1912.80.64661170.9590.1850.6720.95100
2.19-2.2613.40.58961270.9720.1640.6120.946100
2.26-2.3314.50.50461390.9810.1350.5220.953100
2.33-2.4114.50.4361250.9860.1150.4450.965100
2.41-2.5114.20.3461580.990.0920.3530.972100
2.51-2.6313.80.28561190.9910.0780.2960.986100
2.63-2.7613.30.21561510.9930.060.2231.027100
2.76-2.9414.60.1661630.9960.0420.1651.034100
2.94-3.1614.50.12161480.9970.0330.1261.064100
3.16-3.4813.60.08961600.9970.0250.0921.101100
3.48-3.9914.40.07361820.9980.020.0761.142100
3.99-5.02140.06761940.9980.0180.0691.183100
5.02-5013.70.06762880.9980.0190.071.153100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data scaling
SBC-Collectdata collection
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VWW

6vww


Resolution: 1.85→45.19 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1889 5676 4.96 %
Rwork0.1658 108782 -
obs0.1669 114458 93.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.28 Å2 / Biso mean: 25.6454 Å2 / Biso min: 5.47 Å2
Refinement stepCycle: final / Resolution: 1.85→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5489 0 123 718 6330
Biso mean--40.43 33.75 -
Num. residues----695
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.870.2654950.26282019211452
1.87-1.890.28691080.24512340244859
1.89-1.920.26641400.22652579271967
1.92-1.940.25051600.21712770293072
1.94-1.970.24171690.2123055322479
1.97-1.990.2371760.20273237341384
1.99-2.020.22472180.20673493371191
2.02-2.050.22531630.19683663382694
2.05-2.090.21112200.20133753397397
2.09-2.120.22741840.19953870405499
2.12-2.160.21421880.187639244112100
2.16-2.20.2121820.176838874069100
2.2-2.240.18581960.173938984094100
2.24-2.280.20552440.176638204064100
2.28-2.330.21842340.173238704104100
2.33-2.390.18642050.170838594064100
2.39-2.450.19982130.167438904103100
2.45-2.510.19022110.167438814092100
2.51-2.590.19622050.169238674072100
2.59-2.670.19812160.171538654081100
2.67-2.770.20312030.166138974100100
2.77-2.880.20331960.172339244120100
2.88-3.010.18711930.170638984091100
3.01-3.170.19141970.163338954092100
3.17-3.360.18062110.162139074118100
3.36-3.620.16991630.153339334096100
3.62-3.990.17671890.142139344123100
3.99-4.560.12892060.126739124118100
4.57-5.750.14691920.134339484140100
5.75-45.190.17651990.158239944193100
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)
10.1310.02850.04770.02510.02060.12590.0317-0.0111-0.14950.01060.0461-0.16540.00130.07620.03320.09450.0019-0.00880.0786-0.02730.154-59.860924.7317-14.3724
20.0302-0.0147-0.00080.02660.01670.01310.03670.1018-0.0484-0.16830.0157-0.0372-0.0412-0.00740.04130.21870.0012-0.0603-0.0207-0.1447-0.0012-83.132622.8942-37.3064
30.0575-0.0176-0.00420.0293-0.01080.0123-0.02120.0359-0.1307-0.09160.01840.0335-0.0458-0.03930.00220.16370.0138-0.03820.1032-0.04360.1524-87.630615.7196-31.405
40.06850.05810.02590.0551-0.00350.0542-0.0102-0.0042-0.0890.06920.02510.04780.0172-0.0586-0.00980.13380.00760.00710.07580.03310.0934-79.199219.909913.217
50.00350.0041-0.00190.0023-0.00090.0020.0172-0.0133-0.05990.0186-0.0176-0.02640.00270.013300.23460.0109-0.03650.11930.0410.2209-63.770816.053127.0034
60.00010.00320.0030.01830.02260.03060.0464-0.14960.00840.1480.0046-0.04340.03020.01180.03650.3648-0.0973-0.14380.21030.05560.0018-56.626833.676536.2
70.003-0.0033-0.00260.03380.03250.02980.0312-0.0146-0.04910.05740.0454-0.0732-0.00710.05310.02870.2044-0.0252-0.12290.14720.050.2077-49.023221.900931.5467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 187 )A0 - 187
2X-RAY DIFFRACTION2chain 'A' and (resid 188 through 276 )A188 - 276
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 347 )A277 - 347
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 183 )B0 - 183
5X-RAY DIFFRACTION5chain 'B' and (resid 184 through 203 )B184 - 203
6X-RAY DIFFRACTION6chain 'B' and (resid 204 through 292 )B204 - 292
7X-RAY DIFFRACTION7chain 'B' and (resid 293 through 346 )B293 - 346

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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

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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

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