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- PDB-3prp: Structural analysis of a viral OTU domain protease from the Crime... -

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Basic information

Entry
Database: PDB / ID: 3prp
TitleStructural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin
Components
  • Polyubiquitin-B (Fragment)
  • RNA-directed RNA polymerase L
KeywordsHYDROLASE/HYDROLASE / ubiquitin hydrolase / deubiquitinase / hydrolase / cysteine protease / viral protein / HYDROLASE-HYDROLASE complex
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / Hydrolases; Acting on ester bonds / ribosome / structural constituent of ribosome ...RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / Hydrolases; Acting on ester bonds / ribosome / structural constituent of ribosome / RNA-directed RNA polymerase / translation / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / RNA-directed RNA polymerase, nairovirus / Cathepsin B; Chain A - #80 / 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. ...: / RNA-directed RNA polymerase, nairovirus / Cathepsin B; Chain A - #80 / 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. / Cathepsin B; Chain A / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin B / RNA-directed RNA polymerase L / RNA-directed RNA polymerase L / 60S ribosomal protein L40
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.699 Å
AuthorsCapodagli, G.C. / McKercher, M.A. / Baker, E.A. / Masters, E.M. / Brunzelle, J.S. / Pegan, S.D.
CitationJournal: J.Virol. / Year: 2011
Title: Structural analysis of a viral ovarian tumor domain protease from the crimean-congo hemorrhagic Fever virus in complex with covalently bonded ubiquitin.
Authors: Capodagli, G.C. / McKercher, M.A. / Baker, E.A. / Masters, E.M. / Brunzelle, J.S. / Pegan, S.D.
History
DepositionNov 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Feb 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_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_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: Polyubiquitin-B (Fragment)
C: RNA-directed RNA polymerase L
D: Polyubiquitin-B (Fragment)


Theoretical massNumber of molelcules
Total (without water)58,0534
Polymers58,0534
Non-polymers00
Water8,863492
1
A: RNA-directed RNA polymerase L
B: Polyubiquitin-B (Fragment)


Theoretical massNumber of molelcules
Total (without water)29,0272
Polymers29,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-8 kcal/mol
Surface area11420 Å2
MethodPISA
2
C: RNA-directed RNA polymerase L
D: Polyubiquitin-B (Fragment)


Theoretical massNumber of molelcules
Total (without water)29,0272
Polymers29,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-9 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.316, 105.845, 113.032
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase


Mass: 20386.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus / Strain: IbAr10200 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6TQR6, UniProt: Q6TFZ7*PLUS, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, Hydrolases; Acting on ester bonds, RNA-directed RNA polymerase
#2: Protein Polyubiquitin-B (Fragment)


Mass: 8639.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus / References: UniProt: J3QS39, UniProt: Q9PT09*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22-28% PEG 8000, 100 mM Na cacodylate pH 6.5, 100-250 mM Mg acetate, and 2% n-Octyl- -D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.699→77.26 Å / Num. obs: 50853 / % possible obs: 96.5 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.699→1.76 Å / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 2.8 / % possible all: 74.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 28.84 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.21 Å
Translation2.5 Å42.21 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PRM

3prm


Resolution: 1.699→77.26 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2312 / WRfactor Rwork: 0.1871 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8747 / SU B: 4.676 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1163 / SU Rfree: 0.1134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2581 5.1 %RANDOM
Rwork0.172 ---
obs0.174 50853 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 107.21 Å2 / Biso mean: 25.511 Å2 / Biso min: 5.51 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20 Å2
2---0.43 Å2-0 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 1.699→77.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3788 0 8 492 4288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224114
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9595598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8815520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73124.455202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55315735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1761528
X-RAY DIFFRACTIONr_chiral_restr0.0920.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213184
X-RAY DIFFRACTIONr_mcbond_it0.6251.52509
X-RAY DIFFRACTIONr_mcangle_it1.13624093
X-RAY DIFFRACTIONr_scbond_it1.98531605
X-RAY DIFFRACTIONr_scangle_it3.1384.51505
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 132 -
Rwork0.253 2628 -
all-2760 -
obs--72.01 %
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)
13.1613-1.4911-0.39388.4340.74283.6121-0.0928-0.1045-0.05060.58270.1798-0.3850.26740.1946-0.0870.1108-0.0062-0.02690.0992-0.01180.023928.61250.364850.7788
20.5067-1.7946-1.58036.48275.60844.96210.0966-0.03610.1345-0.42720.2652-0.5172-0.25970.1462-0.36170.159-0.07470.08490.1668-0.03990.199633.1102-4.349240.7173
32.9381-1.6353-0.12292.49670.14680.67450.00190.1543-0.1902-0.12290.00220.32670.0632-0.1754-0.00410.0564-0.0235-0.00140.0895-0.00140.055410.6842-2.964436.5882
48.3004-1.5879-0.88546.0963-0.09272.63420.1051-0.36320.82510.0530.00840.1485-0.41820.0933-0.11350.1430.0074-0.01170.1096-0.0480.183213.854216.925143.8044
52.5725-1.20390.3142.155-0.49792.4478-0.02290.07640.1865-0.07970.02630.1861-0.1497-0.2842-0.00330.0579-0.001-0.00840.0640.00210.065612.58457.67838.8067
619.8019-12.9772-8.87415.30949.056721.98370.71871.6772-0.0161-1.5774-0.4634-1.0679-0.08310.8461-0.25530.25580.0030.15480.3186-0.04960.245231.8084-1.444835.4573
71.5995-0.39491.10372.47111.08191.53440.0135-0.0119-0.07760.07080.0562-0.00530.05310.0223-0.06970.0291-0.01210.00780.0355-0.00330.007421.2697-3.073141.4838
820.4993-0.176111.284120.3676-5.105710.07440.2758-1.1483-0.14281.0075-0.1672-0.24150.1922-0.2783-0.10860.13730.00140.020.1042-0.00310.098125.1135-18.077245.6056
95.027-0.4571-1.04574.8505-0.11642.15880.07310.04760.4409-0.042-0.0439-0.0031-0.0771-0.0652-0.02920.0708-0.0147-0.01320.08210.00950.13837.987420.102340.6763
106.05470.06774.69673.77241.27665.31280.04890.46050.109-0.29640.0460.0176-0.00960.3868-0.0950.1198-0.0021-0.00380.19640.05770.083833.489217.368232.4175
115.66211.5131-0.32193.8685-0.36531.43760.1566-0.46491.04610.3739-0.06670.2089-0.3338-0.0618-0.08990.1465-0.00460.03890.1221-0.03670.259631.52622.166946.4163
1210.28167.20784.3856.9394.59673.0996-0.0001-0.0063-0.0859-0.03620.0428-0.0735-0.02960.0294-0.04270.0748-0.0007-0.01130.10230.01470.042425.05610.489238.1443
139.2498-4.46376.78832.4481-2.37947.7843-0.30060.98410.2806-0.3615-0.2425-0.1042-2.07990.78940.54311.1644-0.2118-0.04460.8337-0.12850.185740.842911.14955.2722
144.23571.4190.79621.81580.34691.19950.05070.2453-0.2112-0.1078-0.021-0.08980.00750.0395-0.02970.12770.0378-0.00990.10510.01540.083433.83699.462710.7574
152.84440.26560.21472.8208-0.1520.86730.0363-0.05820.09560.0709-0.03440.2668-0.0453-0.0427-0.00190.08040.02420.01210.04530.0250.060118.908522.467216.6079
164.2812-2.8069-1.04697.66092.41813.3253-0.00390.0147-0.48480.0655-0.01550.68830.3462-0.10250.01940.1133-0.01160.01250.15950.04660.26766.779510.804917.1233
173.5579-0.418-0.72432.0749-0.12541.88830.09370.06670.1230.00610.0080.2255-0.1052-0.0329-0.10170.07390.0062-0.01890.0480.01190.073919.239516.52714.405
1811.2331-0.32022.00766.43910.11347.5250.2101-1.1591-0.67160.7624-0.0086-0.44670.44380.3083-0.20150.20220.0069-0.03110.19620.03490.126133.42017.830817.2404
194.21320.24650.45743.37711.15653.14810.03380.2309-0.0461-0.14850.0068-0.15820.01810.1416-0.04050.06380.0261-0.01810.050.01050.058930.550816.785114.5451
2011.3804-1.4524-14.368726.97210.836845.87990.67871.18311.1956-1.197-0.0245-0.1888-0.56860.174-0.65420.15210.02130.02110.3080.1680.342543.805323.172910.7084
215.9717-0.596-1.81132.95190.10075.241-0.26740.1628-0.42880.09520.04890.06170.3526-0.33210.21850.1371-0.02170.02530.096-0.03950.10423.2824-11.246916.1698
223.8412-0.30711.16663.80930.223610.0522-0.04910.28450.0353-0.1285-0.03440.23620.0123-0.27630.08350.1073-0.01590.0240.1072-0.01980.087719.6356-2.73414.2116
238.6295-3.4272-1.035311.62260.07680.97950.08370.6467-0.3581-0.4805-0.28230.92510.2419-0.55970.19860.2685-0.1754-0.01380.4803-0.1150.278813.0358-11.71719.0311
242.0847-0.7142-1.286914.42369.59067.7899-0.14530.3119-0.19960.30880.2534-0.22070.34420.0172-0.10810.1249-0.0061-0.00380.1285-0.00580.073623.1311-2.615513.15
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 17
2X-RAY DIFFRACTION2A18 - 26
3X-RAY DIFFRACTION3A27 - 70
4X-RAY DIFFRACTION4A71 - 85
5X-RAY DIFFRACTION5A86 - 120
6X-RAY DIFFRACTION6A121 - 131
7X-RAY DIFFRACTION7A132 - 157
8X-RAY DIFFRACTION8A158 - 162
9X-RAY DIFFRACTION9B1 - 26
10X-RAY DIFFRACTION10B27 - 39
11X-RAY DIFFRACTION11B40 - 67
12X-RAY DIFFRACTION12B68 - 75
13X-RAY DIFFRACTION13C2 - 8
14X-RAY DIFFRACTION14C9 - 30
15X-RAY DIFFRACTION15C31 - 78
16X-RAY DIFFRACTION16C79 - 92
17X-RAY DIFFRACTION17C93 - 119
18X-RAY DIFFRACTION18C120 - 133
19X-RAY DIFFRACTION19C134 - 157
20X-RAY DIFFRACTION20C158 - 162
21X-RAY DIFFRACTION21D1 - 33
22X-RAY DIFFRACTION22D34 - 51
23X-RAY DIFFRACTION23D52 - 62
24X-RAY DIFFRACTION24D63 - 75

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