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- PDB-5v5i: OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ub... -

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Basic information

Entry
Database: PDB / ID: 5v5i
TitleOTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.1
Components
  • RNA-directed RNA polymerase L
  • Ubiquitin variant CC.1
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 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 / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity ...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 / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / metal ion binding
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.201 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: To be published
Title: OTU protease of Crimean Congo Hemorrhagic Fever Virus bound to ubiquitin variant CC.1
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 1.3Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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: Ubiquitin variant CC.1
C: RNA-directed RNA polymerase L
D: Ubiquitin variant CC.1


Theoretical massNumber of molelcules
Total (without water)63,6294
Polymers63,6294
Non-polymers00
Water2,558142
1
A: RNA-directed RNA polymerase L
B: Ubiquitin variant CC.1


Theoretical massNumber of molelcules
Total (without water)31,8152
Polymers31,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-7 kcal/mol
Surface area10750 Å2
MethodPISA
2
C: RNA-directed RNA polymerase L
D: Ubiquitin variant CC.1


Theoretical massNumber of molelcules
Total (without water)31,8152
Polymers31,8152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-10 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.167, 83.222, 150.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 19754.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NOTE: The active site CYS is oxidized to sulfenic acid
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)
Strain: Nigeria/IbAr10200/1970 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1, RNA-directed RNA polymerase
#2: Protein Ubiquitin variant CC.1


Mass: 12060.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 30% (w/v) PEG6000, 1.0M lithium chloride and 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 18, 2014 / Details: Osmic VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→43.05 Å / Num. obs: 26471 / % possible obs: 99.6 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Net I/σ(I): 12.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.78 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2328: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→40.167 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2727 2000 7.57 %
Rwork0.222 --
obs0.2259 26414 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→40.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 0 142 3884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023818
X-RAY DIFFRACTIONf_angle_d0.4925170
X-RAY DIFFRACTIONf_dihedral_angle_d13.3542280
X-RAY DIFFRACTIONf_chiral_restr0.042581
X-RAY DIFFRACTIONf_plane_restr0.002665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2007-2.25570.39561360.33021654X-RAY DIFFRACTION96
2.2557-2.31670.35321400.30071710X-RAY DIFFRACTION100
2.3167-2.38490.33161390.28391713X-RAY DIFFRACTION100
2.3849-2.46180.33321410.26251710X-RAY DIFFRACTION100
2.4618-2.54980.32131410.24971724X-RAY DIFFRACTION100
2.5498-2.65190.30481430.25321744X-RAY DIFFRACTION100
2.6519-2.77260.32231400.25991716X-RAY DIFFRACTION100
2.7726-2.91870.33371420.25571731X-RAY DIFFRACTION100
2.9187-3.10150.29631440.25551758X-RAY DIFFRACTION100
3.1015-3.34090.29741430.22361745X-RAY DIFFRACTION100
3.3409-3.67690.2311440.20231757X-RAY DIFFRACTION100
3.6769-4.20840.21531450.17881766X-RAY DIFFRACTION100
4.2084-5.30020.21181470.15641791X-RAY DIFFRACTION100
5.3002-40.17370.22931550.19821895X-RAY DIFFRACTION99

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