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- PDB-6dx3: Crystal structure of the viral OTU domain protease from Taggert virus -

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Basic information

Entry
Database: PDB / ID: 6dx3
TitleCrystal structure of the viral OTU domain protease from Taggert virus
ComponentsRNA-dependent RNA polymerase
KeywordsHYDROLASE / PROTEIN BINDING / viral OTU / DUB / Viral Protein
Function / homology
Function and homology information


RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription
Similarity search - Function
: / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesTaggert virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.052 Å
AuthorsDzimianski, J.V. / Beldon, B.S. / Daczkowski, C.M. / Goodwin, O.Y. / Pegan, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI109008 United States
CitationJournal: PLoS Pathog. / Year: 2019
Title: Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity.
Authors: Dzimianski, J.V. / Beldon, B.S. / Daczkowski, C.M. / Goodwin, O.Y. / Scholte, F.E.M. / Bergeron, E. / Pegan, S.D.
History
DepositionJun 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
C: RNA-dependent RNA polymerase
D: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1846
Polymers82,1364
Non-polymers492
Water7,098394
1
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5582
Polymers20,5341
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)20,5341
Polymers20,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)20,5341
Polymers20,5341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5582
Polymers20,5341
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.163, 60.948, 66.501
Angle α, β, γ (deg.)64.95, 89.84, 84.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
RNA-dependent RNA polymerase


Mass: 20533.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taggert virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A142J8F6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.15 M magnesium formate, 22% PEG 3350, 0.25 M TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 40280 / % possible obs: 97.4 % / Redundancy: 3.6 % / CC1/2: 0.99 / Net I/σ(I): 17.3
Reflection shellResolution: 2.05→2.09 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3634 / CC1/2: 0.847

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HXD

4hxd


Resolution: 2.052→36.462 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 29.13
RfactorNum. reflection% reflection
Rfree0.2501 1934 4.81 %
Rwork0.2274 --
obs0.2285 40237 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.052→36.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5374 0 2 394 5770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055520
X-RAY DIFFRACTIONf_angle_d0.7097487
X-RAY DIFFRACTIONf_dihedral_angle_d22.2452031
X-RAY DIFFRACTIONf_chiral_restr0.054776
X-RAY DIFFRACTIONf_plane_restr0.004974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.052-2.10330.32351060.27862426X-RAY DIFFRACTION84
2.1033-2.16020.26551560.25822679X-RAY DIFFRACTION96
2.1602-2.22380.29651260.25672736X-RAY DIFFRACTION96
2.2238-2.29550.34451370.27142780X-RAY DIFFRACTION98
2.2955-2.37760.31641050.25752764X-RAY DIFFRACTION96
2.3776-2.47270.2681400.25362776X-RAY DIFFRACTION97
2.4727-2.58520.28481270.24412752X-RAY DIFFRACTION98
2.5852-2.72150.29251850.25562759X-RAY DIFFRACTION98
2.7215-2.8920.3041390.24352771X-RAY DIFFRACTION97
2.892-3.11510.26531520.2332729X-RAY DIFFRACTION97
3.1151-3.42840.23441400.20932754X-RAY DIFFRACTION98
3.4284-3.9240.21491290.20362802X-RAY DIFFRACTION98
3.924-4.94190.18471560.18972754X-RAY DIFFRACTION99
4.9419-36.4680.24691360.22742821X-RAY DIFFRACTION98
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)
12.7809-0.9252.08375.4276-4.18454.5943-0.1961-0.51090.58420.09180.3876-0.0269-0.4682-0.4736-0.14770.30280.06130.07150.4335-0.14060.2375-13.7668-25.7331-26.325
27.0764-4.8686-0.62796.96052.77475.8930.53570.58210.3698-0.9586-0.377-0.1303-0.3426-0.1896-0.1740.19830.00470.04320.30940.03910.2358-6.9293-29.4493-44.8521
36.8972-3.5034-2.27144.78643.998.52560.35211.3670.2286-0.2901-0.1374-0.3311-0.0855-0.1439-0.09070.2050.04770.04290.3815-0.00640.20072.7463-35.7234-41.9159
42.5168-0.4491-1.09662.23390.12455.45680.11380.3649-0.5532-0.0801-0.00150.00170.25590.0826-0.11520.14960.0045-0.03510.2584-0.07310.2332-3.2673-45.1848-29.7007
50.6238-0.1896-0.37993.5840.58274.5274-0.0447-0.04920.2212-0.0099-0.07130.1362-0.1784-0.21080.130.14680.00260.02180.2896-0.050.234-8.7164-28.7613-35.3377
63.5287-4.71612.32997.79110.13728.60660.21920.63032.40010.9008-0.2416-0.8019-1.80820.95250.14840.7065-0.04110.110.48270.04960.73413.4845-21.4149-40.846
73.6482-0.1408-1.09985.06261.35233.01070.0770.17460.2804-0.1964-0.01360.0566-0.24740.0043-0.09610.12330.0159-0.02430.26190.00730.1718-17.4588-41.5681-61.7803
82.40450.9197-0.56842.8463-0.43791.31150.0271-0.20780.05190.0646-0.0587-0.05860.00310.04960.03330.13360.0394-0.0140.2663-0.05290.1495-18.412-49.8279-58.0841
97.8862.13920.54320.94321.50825.20170.13380.85381.5416-0.6092-0.18290.8949-0.3941-0.64440.09150.57080.11660.09520.57130.31840.7795-28.9764-34.9816-65.7457
101.8647-0.2518-1.33043.4836-2.61084.0787-0.0960.2223-0.3145-0.15120.17840.22760.3812-0.2469-0.00790.3-0.0987-0.040.3929-0.10350.2596-37.4504-55.8241-30.0702
114.80713.0367-0.01659.06062.84252.63150.3122-0.6271-0.19061.0572-0.39820.42520.3529-0.30650.05070.2401-0.0317-0.05320.39370.0280.215-30.3818-52.161-11.5901
122.11270.8431.14012.1749-1.66178.10090.1965-0.2183-0.0230.1685-0.1838-0.14-0.27220.62980.0210.1299-0.0040.00970.3242-0.09010.2272-21.271-41.1118-20.7369
133.8824-0.14210.31795.86160.73185.12860.1399-0.06030.37430.13330.04850.257-0.0705-0.2845-0.1940.12110.00960.00340.3056-0.05750.2293-29.6243-36.1165-26.9294
145.92490.8473-1.69944.42150.27456.3422-0.06790.1417-0.45950.0474-0.03010.12330.2256-0.30040.11430.14880.0036-0.05080.1606-0.0160.1873-32.2847-52.8117-21.0791
156.5858-6.3182-4.43936.79566.51469.9588-0.6290.1073-1.3553-0.32980.79960.10030.3846-0.0913-0.16320.4552-0.09030.04540.45180.02780.5565-18.953-59.3533-18.1677
164.1088-2.6367-0.69123.45263.26444.5876-0.2654-0.6842-0.15290.64230.516-0.31140.392-0.1367-0.31090.23880.0023-0.02820.4573-0.08080.245513.1963-63.0243-45.4219
173.2445-2.08711.64645.3277-3.25467.75750.30620.1858-0.4893-0.1261-0.18760.320.4017-0.0508-0.13310.1588-0.0192-0.02820.2679-0.06450.28851.3349-71.7152-61.783
182.45410.3021-0.56365.19442.10152.74460.03990.48870.0281-0.17220.0142-0.1984-0.12770.0094-0.05890.14670.0282-0.00920.3206-0.01910.20442.6717-53.2914-62.626
199.2921-3.5-0.96067.45570.41826.186-0.1926-0.6293-0.41550.35750.11330.16740.05840.06720.09890.2139-0.0289-0.0130.25480.00380.18428.3086-66.8841-50.5357
205.80670.5996-2.54326.8264-2.28129.1651-0.0759-0.283-0.56260.0094-0.0349-0.4660.26350.47770.06630.12650.0249-0.02830.2002-0.03760.24437.7592-70.1558-58.6123
214.35280.44081.37024.7781-1.37134.3238-0.3268-0.86-1.50880.85330.30331.11571.1525-0.56280.04410.6939-0.15540.08740.66810.32560.7595-5.3147-74.5462-50.6828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 39 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 56 )
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 156 )
6X-RAY DIFFRACTION6chain 'A' and (resid 157 through 165 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 56 )
8X-RAY DIFFRACTION8chain 'B' and (resid 57 through 156 )
9X-RAY DIFFRACTION9chain 'B' and (resid 157 through 167 )
10X-RAY DIFFRACTION10chain 'C' and (resid 5 through 24 )
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 39 )
12X-RAY DIFFRACTION12chain 'C' and (resid 40 through 75 )
13X-RAY DIFFRACTION13chain 'C' and (resid 76 through 112 )
14X-RAY DIFFRACTION14chain 'C' and (resid 113 through 156 )
15X-RAY DIFFRACTION15chain 'C' and (resid 157 through 167 )
16X-RAY DIFFRACTION16chain 'D' and (resid 5 through 24 )
17X-RAY DIFFRACTION17chain 'D' and (resid 25 through 56 )
18X-RAY DIFFRACTION18chain 'D' and (resid 57 through 112 )
19X-RAY DIFFRACTION19chain 'D' and (resid 113 through 141 )
20X-RAY DIFFRACTION20chain 'D' and (resid 142 through 156 )
21X-RAY DIFFRACTION21chain 'D' and (resid 157 through 168 )

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