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- PDB-5uv5: Crystal Structure of a 2-Hydroxyisoquinoline-1,3-dione RNase H Ac... -

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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 / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / 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 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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

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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: 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

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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

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Phasing

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

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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

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  • 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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