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- PDB-5jze: Erve virus viral OTU domain protease in complex with mouse ISG15 -

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Basic information

Entry
Database: PDB / ID: 5jze
TitleErve virus viral OTU domain protease in complex with mouse ISG15
Components
  • RNA-dependent RNA polymerase
  • Ubiquitin-like protein ISG15
KeywordsHYDROLASE / vOTU / ISG15 / nairovirus / protease
Function / homology
Function and homology information


positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication ...positive regulation of protein oligomerization / Termination of translesion DNA synthesis / ISG15 antiviral mechanism / ISG15-protein conjugation / PKR-mediated signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / response to bacterium / response to virus / modification-dependent protein catabolic process / positive regulation of type II interferon production / protein tag activity / integrin binding / defense response to virus / defense response to bacterium / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / ubiquitin protein ligase binding / extracellular region / cytoplasm
Similarity search - Function
: / Cathepsin B; Chain A - #80 / : / 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 ...: / Cathepsin B; Chain A - #80 / : / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
prop-2-en-1-amine / CITRATE ANION / RNA-directed RNA polymerase L / Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesMus musculus (house mouse)
Erve virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsDeaton, M.K. / Dzimianski, J.V. / Pegan, S.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI109008 United States
United States Department of Agriculture (USDA)58-5030-5-034 United States
CitationJournal: J.Virol. / Year: 2016
Title: Biochemical and Structural Insights into the Preference of Nairoviral DeISGylases for Interferon-Stimulated Gene Product 15 Originating from Certain Species.
Authors: Deaton, M.K. / Dzimianski, J.V. / Daczkowski, C.M. / Whitney, G.K. / Mank, N.J. / Parham, M.M. / Bergeron, E. / Pegan, S.D.
History
DepositionMay 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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.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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ubiquitin-like protein ISG15
A: RNA-dependent RNA polymerase
D: Ubiquitin-like protein ISG15
C: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,86010
Polymers53,9894
Non-polymers8716
Water4,558253
1
B: Ubiquitin-like protein ISG15
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4305
Polymers26,9952
Non-polymers4353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-6 kcal/mol
Surface area11700 Å2
MethodPISA
2
D: Ubiquitin-like protein ISG15
C: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4305
Polymers26,9952
Non-polymers4353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-4 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.992, 65.992, 121.992
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein


Mass: 8981.304 Da / Num. of mol.: 2 / Fragment: C-terminal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Isg15, G1p2, Ucrp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64339
#2: Protein RNA-dependent RNA polymerase


Mass: 18013.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erve virus / Gene: RdRP / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: J3RTH4
#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N
#4: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 6% PEG 6000 and 0.1 M citric acid supplemented 0.2% of 3.0 M NTSB-195

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→65.99 Å / Num. obs: 18742 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.119 / Net I/av σ(I): 11.541 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.47-2.513.70.481100
2.51-2.5640.4861100
2.56-2.614.30.4251100
2.61-2.664.20.4161100
2.66-2.724.20.3281100
2.72-2.784.20.309199.9
2.78-2.854.30.262199.9
2.85-2.934.30.2411100
2.93-3.014.30.2011100
3.01-3.114.30.1571100
3.11-3.224.30.1331100
3.22-3.354.30.111100
3.35-3.54.30.0991100
3.5-3.694.30.0821100
3.69-3.924.30.0741100
3.92-4.224.30.0641100
4.22-4.654.30.0681100
4.65-5.324.30.0841100
5.32-6.74.20.0861100
6.7-504.20.035199.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HXD

4hxd


Resolution: 2.47→65.99 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.227 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.828 / ESU R Free: 0.275
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 986 5.3 %RANDOM
Rwork0.1737 ---
obs0.1767 17722 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.12 Å2 / Biso mean: 24.713 Å2 / Biso min: 6.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.67 Å20 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 2.47→65.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 60 253 4108
Biso mean--53.1 23.08 -
Num. residues----469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193969
X-RAY DIFFRACTIONr_bond_other_d0.0080.023757
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.9665362
X-RAY DIFFRACTIONr_angle_other_deg0.87338606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6155473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13823.762202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54615691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3721532
X-RAY DIFFRACTIONr_chiral_restr0.0860.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024507
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02965
X-RAY DIFFRACTIONr_mcbond_it1.5962.2971886
X-RAY DIFFRACTIONr_mcbond_other1.5962.2961885
X-RAY DIFFRACTIONr_mcangle_it2.6343.4352355
LS refinement shellResolution: 2.472→2.536 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 80 -
Rwork0.232 1307 -
all-1387 -
obs--100 %

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