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- PDB-5v5g: OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ub... -

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Basic information

Entry
Database: PDB / ID: 5v5g
TitleOTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.4
Components
  • RNA-directed RNA polymerase L
  • Ubiquitin variant CC.4
Keywordshydrolase / transferase / Ovarian Tumor Domain protease / deubiquitinase / ubiquitin variant
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / Hydrolases; Acting on ester bonds / ubiquitinyl hydrolase 1 ...RNA-templated viral transcription / negative stranded viral RNA replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein deubiquitination / endoplasmic reticulum unfolded protein response / ERAD pathway / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / Hydrolases; Acting on ester bonds / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / metal ion binding
Similarity search - Function
RNA-directed RNA polymerase, nairovirus / : / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase ...RNA-directed RNA polymerase, nairovirus / : / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / RNA-directed RNA polymerase L, N-terminal / L protein N-terminus / 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 / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhare, B. / Mark, B.L.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2015-05310 Canada
Research Manitoba Canada
CitationJournal: PLoS Pathog. / Year: 2017
Title: Potent and selective inhibition of pathogenic viruses by engineered ubiquitin variants.
Authors: Zhang, W. / Bailey-Elkin, B.A. / Knaap, R.C.M. / Khare, B. / Dalebout, T.J. / Johnson, G.G. / van Kasteren, P.B. / McLeish, N.J. / Gu, J. / He, W. / Kikkert, M. / Mark, B.L. / Sidhu, S.S.
History
DepositionMar 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: Ubiquitin variant CC.4
C: RNA-directed RNA polymerase L
D: Ubiquitin variant CC.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,69611
Polymers66,3794
Non-polymers3177
Water3,819212
1
A: RNA-directed RNA polymerase L
B: Ubiquitin variant CC.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3996
Polymers33,1892
Non-polymers2094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA-directed RNA polymerase L
D: Ubiquitin variant CC.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2975
Polymers33,1892
Non-polymers1083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.312, 64.312, 277.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 21084.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)
Strain: Nigeria/IbAr10200/1970 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1, RNA-directed RNA polymerase
#2: Protein Ubiquitin variant CC.4


Mass: 12104.788 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% (w/v) PEG3350, 0.1 M Tris pH 7.0, 0.2 M sodium chloride and Silver Bullet formulation #G1 (0.16% (w/v) each of 5-Sulfosalicylic acid dehydrate, dodecanedioic acid, hippuric acid, ...Details: 25% (w/v) PEG3350, 0.1 M Tris pH 7.0, 0.2 M sodium chloride and Silver Bullet formulation #G1 (0.16% (w/v) each of 5-Sulfosalicylic acid dehydrate, dodecanedioic acid, hippuric acid, mellitic acid, oxalacetic acid, suberic acid and 0.02 M HEPES sodium pH 6.8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→47.17 Å / Num. obs: 34979 / % possible obs: 99.5 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2828 / CC1/2: 0.926 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2328: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PT2

3pt2


Resolution: 2.1→47.17 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1998 5.73 %
Rwork0.1744 --
obs0.1775 34878 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 19 212 4109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013982
X-RAY DIFFRACTIONf_angle_d1.045387
X-RAY DIFFRACTIONf_dihedral_angle_d13.8682362
X-RAY DIFFRACTIONf_chiral_restr0.057599
X-RAY DIFFRACTIONf_plane_restr0.007686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.15260.33121400.24612307X-RAY DIFFRACTION99
2.1526-2.21080.30371420.21642315X-RAY DIFFRACTION99
2.2108-2.27580.25871390.20892273X-RAY DIFFRACTION99
2.2758-2.34930.2971390.19392287X-RAY DIFFRACTION99
2.3493-2.43320.26391400.18972311X-RAY DIFFRACTION99
2.4332-2.53070.25211430.18042337X-RAY DIFFRACTION100
2.5307-2.64580.25051400.192314X-RAY DIFFRACTION99
2.6458-2.78530.25971430.19092351X-RAY DIFFRACTION99
2.7853-2.95980.28121400.19442326X-RAY DIFFRACTION99
2.9598-3.18830.24981440.19722360X-RAY DIFFRACTION99
3.1883-3.5090.22591430.16792367X-RAY DIFFRACTION99
3.509-4.01660.20131440.15712380X-RAY DIFFRACTION98
4.0166-5.05950.16411460.1362398X-RAY DIFFRACTION98
5.0595-47.18190.22041550.17392554X-RAY DIFFRACTION97

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