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- PDB-3pse: Structure of a viral OTU domain protease bound to interferon-stim... -

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Basic information

Entry
Database: PDB / ID: 3pse
TitleStructure of a viral OTU domain protease bound to interferon-stimulated gene 15 (ISG15)
Components
  • RNA polymerase
  • Ubiquitin-like protein ISG15
KeywordsHYDROLASE/PROTEIN BINDING / viral deubiquitinase / 3-aminopropane / intein-mediated ligation / Crimean-Congo Hemorrhagic Fever virus / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


ISG15-protein conjugation / positive regulation of protein oligomerization / RNA-templated viral transcription / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / negative stranded viral RNA replication / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway ...ISG15-protein conjugation / positive regulation of protein oligomerization / RNA-templated viral transcription / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / negative stranded viral RNA replication / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / positive regulation of interleukin-10 production / protein deubiquitination / positive regulation of bone mineralization / endoplasmic reticulum unfolded protein response / ERAD pathway / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / modification-dependent protein catabolic process / ISG15 antiviral mechanism / response to virus / protein tag activity / integrin binding / positive regulation of type II interferon production / Interferon alpha/beta signaling / symbiont-mediated suppression of host ISG15-protein conjugation / defense response to virus / 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 / defense response to bacterium / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / innate immune response / RNA-directed RNA polymerase / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular region / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
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 ...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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin domain / 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
1.7.6 3-bromanylpropan-1-amine / Ubiquitin-like protein ISG15 / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBacik, J.P. / James, T.W. / Frias-Staheli, N. / Garcia-Sastre, A. / Mark, B.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for the removal of ubiquitin and interferon-stimulated gene 15 by a viral ovarian tumor domain-containing protease.
Authors: James, T.W. / Frias-Staheli, N. / Bacik, J.P. / Levingston Macleod, J.M. / Khajehpour, M. / Garcia-Sastre, A. / Mark, B.L.
History
DepositionDec 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0May 31, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,8294
Polymers36,5982
Non-polymers2302
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-10 kcal/mol
Surface area15010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.740, 69.810, 69.670
Angle α, β, γ (deg.)90.00, 93.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RNA polymerase


Mass: 19480.807 Da / Num. of mol.: 1 / Fragment: OTU domain (UNP residues 1-169)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TQF5
#2: 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 / hUCRP


Mass: 17117.611 Da / Num. of mol.: 1 / Mutation: C78S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Production host: Escherichia coli (E. coli) / References: UniProt: P05161
#3: Chemical ChemComp-4LJ / 1.7.6 3-bromanylpropan-1-amine


Mass: 138.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8BrN
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsS83N IS A NATURAL VARIANT

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 100 mM MES, 23% PEG6000, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→34.9 Å / Num. all: 14673 / Num. obs: 14495 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.5 / Redundancy: 3.1 % / Rmerge(I) obs: 0.107 / Rsym value: 0.129 / Net I/σ(I): 7.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.68 / % possible all: 98

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1Z2M AND 3PT2

1z2m

3pt2


Resolution: 2.3→34.671 Å / SU ML: 0.28 / σ(F): 1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 699 5.04 %RANDOM
Rwork0.1635 ---
obs0.1666 13860 93.27 %-
all-14495 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.22 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.904 Å20 Å2-1.0195 Å2
2--1.3748 Å2-0 Å2
3---4.5292 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 10 139 2582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062501
X-RAY DIFFRACTIONf_angle_d0.9443395
X-RAY DIFFRACTIONf_dihedral_angle_d13.604906
X-RAY DIFFRACTIONf_chiral_restr0.06385
X-RAY DIFFRACTIONf_plane_restr0.004439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.47750.2741330.19952465X-RAY DIFFRACTION88
2.4775-2.72680.26411410.19152558X-RAY DIFFRACTION91
2.7268-3.12110.24011360.17572634X-RAY DIFFRACTION93
3.1211-3.93140.20481400.14452752X-RAY DIFFRACTION97
3.9314-34.67460.2051490.15452752X-RAY DIFFRACTION96
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)
12.74-0.15880.85262.24240.47852.33080.0072-0.0455-0.24920.23430.1357-0.10140.07860.0977-0.14850.05340.0177-0.02480.0136-0.01530.12157.6836-17.396440.9201
20.13050.1797-0.74381.2736-0.25529.22090.859-0.125-0.1207-0.4849-0.42540.51380.41842.5348-0.42130.9645-0.3062-0.021.0031-0.14020.4229-20.5406-22.2454-2.8176
30.5005-0.1080.22640.4932-0.09460.1809-0.01830.4365-0.21870.2198-0.2105-0.02260.12340.31830.15810.5997-0.1364-0.10590.6977-0.10470.2607-22.2083-17.35335.6786
41.4910.7251-0.12031.6688-0.28620.8207-0.22620.26870.1078-0.30970.2140.1567-0.04260.10310.00570.1335-0.0363-0.03380.12860.00010.1362-1.5852-5.667921.4522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -1:162)
2X-RAY DIFFRACTION2(chain B and resid 4:19)
3X-RAY DIFFRACTION3(chain B and resid 23:78)
4X-RAY DIFFRACTION4(chain B and resid 79:156)

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