[English] 日本語
Yorodumi
- PDB-5uv5: Crystal Structure of a 2-Hydroxyisoquinoline-1,3-dione RNase H Ac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uv5
TitleCrystal Structure of a 2-Hydroxyisoquinoline-1,3-dione RNase H Active Site Inhibitor with Multiple Binding Modes to HIV Reverse Transcriptase
Components
  • Reverse transcriptase/ribonuclease H
  • p51 RT
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / REVERSE TRANSCRIPTASE / INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-Y55 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsKirby, K.A. / Sarafianos, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100890 United States
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: A 2-Hydroxyisoquinoline-1,3-Dione Active-Site RNase H Inhibitor Binds in Multiple Modes to HIV-1 Reverse Transcriptase.
Authors: Kirby, K.A. / Myshakina, N.A. / Christen, M.T. / Chen, Y.L. / Schmidt, H.A. / Huber, A.D. / Xi, Z. / Kim, S. / Rao, R.K. / Kramer, S.T. / Yang, Q. / Singh, K. / Parniak, M.A. / Wang, Z. / ...Authors: Kirby, K.A. / Myshakina, N.A. / Christen, M.T. / Chen, Y.L. / Schmidt, H.A. / Huber, A.D. / Xi, Z. / Kim, S. / Rao, R.K. / Kramer, S.T. / Yang, Q. / Singh, K. / Parniak, M.A. / Wang, Z. / Ishima, R. / Sarafianos, S.G.
History
DepositionFeb 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H
B: p51 RT
C: Reverse transcriptase/ribonuclease H
D: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,11010
Polymers228,4044
Non-polymers7066
Water00
1
A: Reverse transcriptase/ribonuclease H
B: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5555
Polymers114,2022
Non-polymers3533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-36 kcal/mol
Surface area45260 Å2
MethodPISA
2
C: Reverse transcriptase/ribonuclease H
D: p51 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5555
Polymers114,2022
Non-polymers3533
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-33 kcal/mol
Surface area45570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.990, 88.670, 108.860
Angle α, β, γ (deg.)105.530, 93.410, 110.130
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT


Mass: 64105.441 Da / Num. of mol.: 2 / Fragment: p66 domain residues 600-1154 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: pET35a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H
#2: Protein p51 RT


Mass: 50096.539 Da / Num. of mol.: 2 / Fragment: p51 domain residues 600-1027 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Plasmid: pET35a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P03366
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-Y55 / 7-(furan-2-yl)-2-hydroxyisoquinoline-1,3(2H,4H)-dione


Mass: 243.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9NO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: PEG 3350, SODIUM POTASSIUM PHOSPHATE, ETHYLENE GLYCOL, TRIS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→62.43 Å / Num. obs: 45121 / % possible obs: 98 % / Redundancy: 7.4 % / Biso Wilson estimate: 61.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.036 / Rrim(I) all: 0.096 / Net I/σ(I): 18.3 / Num. measured all: 331908 / Scaling rejects: 2
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.622 / CC1/2: 0.907 / Rpim(I) all: 0.256 / Rrim(I) all: 0.674 / % possible all: 97.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.81 Å62.43 Å
Translation8.81 Å62.43 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHASER2.6.1phasing
PHENIX1.11.1refinement
PDB_EXTRACT3.22data extraction
XDSOct 15, 2015data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J1E

5j1e


Resolution: 3→62.43 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.19
RfactorNum. reflection% reflection
Rfree0.2873 2174 4.82 %
Rwork0.2321 --
obs0.2347 45106 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.77 Å2 / Biso mean: 68.1267 Å2 / Biso min: 9.79 Å2
Refinement stepCycle: final / Resolution: 3→62.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15330 0 40 0 15370
Biso mean--91.87 --
Num. residues----1873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915797
X-RAY DIFFRACTIONf_angle_d0.65521429
X-RAY DIFFRACTIONf_chiral_restr0.0462326
X-RAY DIFFRACTIONf_plane_restr0.0062695
X-RAY DIFFRACTIONf_dihedral_angle_d2.8469505
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0001-3.06530.40011160.33332656277297
3.0653-3.13660.38891320.30162687281997
3.1366-3.2150.34071170.2772672278998
3.215-3.30190.33551640.26822671283597
3.3019-3.39910.34181480.26342629277796
3.3991-3.50880.33621520.25532592274496
3.5088-3.63420.31521250.25082665279097
3.6342-3.77970.29871280.23452702283099
3.7797-3.95170.32281420.21982676281899
3.9517-4.160.26541340.21532723285799
4.16-4.42060.24731400.20072691283199
4.4206-4.76180.24741330.20382696282999
4.7618-5.24070.27731490.21552726287599
5.2407-5.99860.29631460.22712695284199
5.9986-7.55550.26561270.24242726285399
7.5555-62.44630.22821210.21192725284699
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)
1-0.0024-0.03170.04980.0188-0.0020.02690.02310.2201-0.0831-0.12040.03810.0232-0.0243-0.044900.80940.10340.08270.65190.09210.5204-1.644851.0238-60.075
20.03490.0112-0.01060.01330.04680.01550.01110.03390.0697-0.06480.002-0.1313-0.0056-0.003300.42280.03840.08150.4228-0.02770.4376.200641.0072-37.6067
3-0.0108-0.011-0.00410.0066-0.00720.0095-0.04930.0650.04590.069-0.09180.03420.09290.0752-00.72780.16160.07830.54070.04820.289-3.533946.5704-59.6308
40.01680.00190.02130.01630.02080.0455-0.1415-0.015-0.1007-0.04150.2082-0.2546-0.1232-0.163700.46950.00280.12370.4483-0.04150.471810.745131.5698-39.7915
5-0.0429-0.0039-0.0630.0452-0.0164-0.09370.33210.01080.09450.20690.42920.04780.09440.74340-0.0643-0.87560.3042-1.383-0.39580.63928.657461.1057-35.4939
60.0623-0.0055-0.09580.08740.00970.1401-0.0707-0.09290.15450.00870.1018-0.09450.03430.0233-00.186-0.0268-0.02020.2744-0.01680.27572.099853.8196-7.5276
70.1215-0.07420.02910.0777-0.03430.10640.0041-0.0521-0.0105-0.0249-0.0416-0.0619-0.0448-0.0506-00.30230.0478-0.00730.1243-0.03160.2199-18.771577.33022.9395
80.0110.02050.02110.17730.1460.1285-0.0088-0.0002-0.0032-0.0023-0.0293-0.02030.00190.0061-0.00080.7797-0.0105-0.14150.55080.04920.5187-29.751676.3262-3.6498
90.1087-0.0881-0.18250.09460.0340.12990.0160.1121-0.07410.09530.0124-0.02040.0623-0.0445-00.1912-0.0105-0.01550.2061-0.05260.2348-15.200333.6344-28.3374
100.0035-0.01510.0090.033-0.00770.0211-0.0912-0.0007-0.1786-0.04070.01980.32920.13730.065-00.427-0.09550.00260.4536-0.06170.5987-31.59828.6124-19.1262
110.00830.0116-0.02530.0111-0.00070.0346-0.02820.03140.0119-0.0692-0.15110.1233-0.13220.1573-00.3022-0.0705-0.05010.37610.01660.3669-12.181534.2669-33.8654
120.1007-0.1780.13460.0446-0.05310.0275-0.04540.23640.1580.26720.0078-0.15240.2246-0.309-00.4599-0.19590.03450.3644-0.07320.5402-32.243224.7518-12.82
130.0981-0.0561-0.04640.062-0.07190.08860.0667-0.0171-0.31220.08660.09820.1763-0.04640.066400.468-0.07450.07410.48070.01110.553-37.902962.36248.0614
140.0217-0.04090.0680.03980.04610.032-0.023-0.0228-0.0806-0.0461-0.00970.02-0.1624-0.0232-00.0202-0.01420.01420.12240.0490.1266-22.602645.9784-8.3457
150.03840.05390.02070.09920.03980.0948-0.1118-0.04950.02670.05070.17180.00750.0743-0.0206-00.31670.01590.01840.52980.16870.4035-32.725972.2298-24.2457
16-0.01810.0349-0.0053-0.05820.08170.0337-0.0706-0.0592-0.2105-0.03650.0968-0.1367-0.13090.0048-00.43520.0283-0.04180.46360.03190.4627-25.772584.3493-44.6278
17-0.0177-0.01970.04550.0123-0.0011-0.0021-0.0546-0.04680.00630.036-0.12860.1314-0.0477-0.083300.32460.1114-0.21270.35520.4653-0.1699-34.988974.8515-20.6522
180.02150.0249-0.0621-0.00460.01770.0327-0.06080.07190.23960.08760.1951-0.01120.14380.017400.4412-0.0394-0.00380.41280.00050.4472-20.787693.3331-41.9027
190.04520.02550.09860.0542-0.00680.04280.0373-0.16290.1171-0.28740.13480.190.13570.236200.26930.0208-0.08780.28890.03350.4098-25.40664.7478-49.3477
200.0799-0.05110.0124-0.01690.09220.0468-0.09280.2315-0.28790.26270.0723-0.2693-0.1524-0.1517-00.1705-0.02730.10380.4788-0.04870.4574-29.518475.4807-76.5224
210.0391-0.01340.00850.1508-0.01760.06720.12670.16850.2380.14920.2891-0.27460.3312-0.241200.38490.1161-0.12710.1183-0.13970.2921-50.028552.4903-89.0234
220.24590.0013-0.10760.00710.00610.05130.0158-0.01360.01030.00020.00940.00250.0047-0.01180.00040.79650.11340.05650.6086-0.05430.6148-62.262251.4587-82.8039
230.06630.0289-0.04780.13260.07690.05510.0086-0.029-0.1374-0.0141-0.0615-0.1353-0.1157-0.088200.24610.0061-0.00050.18910.01360.1561-46.435991.6772-53.4074
240.0001-0.02640.0229-0.00740.03440.02250.0873-0.20320.11-0.0562-0.11050.0373-0.1778-0.0732-00.56790.0287-0.10480.4927-0.03950.4486-63.994598.3842-62.1171
250.01070.0160.03210.0084-0.01510.02680.089-0.12970.0624-0.00770.02220.0030.11020.110900.22720.0685-0.02660.26970.03630.2708-44.232391.8397-48.0821
260.12370.0519-0.12310.00770.05340.0435-0.1003-0.05950.0239-0.16420.09450.0586-0.19650.0041-00.67560.0765-0.14150.4002-0.04410.3794-64.7276103.2854-67.7885
270.0260.04370.074-0.08280.1240.01020.2908-0.3183-0.0741-0.1950.28790.24730.1286-0.019600.13330.07250.0192-0.1243-0.11110.0318-69.596467.1599-92.7345
280.0257-0.002-0.03350.0754-0.05040.0666-0.0596-0.05150.0331-0.0424-0.0804-0.0026-0.01020.032400.1751-0.00770.00030.2226-0.00240.1219-54.839382.0642-75.2468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain A and resseq 4:84A4 - 84
2X-RAY DIFFRACTION2Chain A and resseq 85:120A85 - 120
3X-RAY DIFFRACTION3Chain A and resseq 121:154A121 - 154
4X-RAY DIFFRACTION4Chain A and resseq 155:215A155 - 215
5X-RAY DIFFRACTION5Chain A and resseq 236:322A236 - 322
6X-RAY DIFFRACTION6Chain A and resseq 323:427A323 - 427
7X-RAY DIFFRACTION7Chain A and resseq 428:553A428 - 553
8X-RAY DIFFRACTION8Chain A and resseq 601:603A601 - 603
9X-RAY DIFFRACTION9Chain B and resseq 1:84B1 - 84
10X-RAY DIFFRACTION10Chain B and resseq 85:120B85 - 120
11X-RAY DIFFRACTION11Chain B and resseq 121:150B121 - 150
12X-RAY DIFFRACTION12Chain B and resseq 151:247B151 - 247
13X-RAY DIFFRACTION13Chain B and resseq 248:323B248 - 323
14X-RAY DIFFRACTION14Chain B and resseq 324:422B324 - 422
15X-RAY DIFFRACTION15Chain C and resseq 3:84C3 - 84
16X-RAY DIFFRACTION16Chain C and resseq 85:120C85 - 120
17X-RAY DIFFRACTION17Chain C and resseq 121:154C121 - 154
18X-RAY DIFFRACTION18Chain C and resseq 155:215C155 - 215
19X-RAY DIFFRACTION19Chain C and resseq 236:322C236 - 322
20X-RAY DIFFRACTION20Chain C and resseq 323:427C323 - 427
21X-RAY DIFFRACTION21Chain C and resseq 428:554C428 - 554
22X-RAY DIFFRACTION22Chain C and resseq 601:603C601 - 603
23X-RAY DIFFRACTION23Chain D and resseq 7:84D7 - 84
24X-RAY DIFFRACTION24Chain D and resseq 85:120D85 - 120
25X-RAY DIFFRACTION25Chain D and resseq 121:150D121 - 150
26X-RAY DIFFRACTION26Chain D and resseq 151:247D151 - 247
27X-RAY DIFFRACTION27Chain D and resseq 248:323D248 - 323
28X-RAY DIFFRACTION28Chain D and resseq 324:427D324 - 427

+
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