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- PDB-6ffa: FMDV Leader protease bound to substrate ISG15 -

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Basic information

Entry
Database: PDB / ID: 6ffa
TitleFMDV Leader protease bound to substrate ISG15
Components
  • Lbpro
  • Ubiquitin-like protein ISG15
KeywordsHYDROLASE / Leader protease / deISGylase / deubiquitinase
Function / homology
Function and homology information


L-peptidase / positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / : / symbiont-mediated perturbation of host chromatin organization / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway ...L-peptidase / positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / : / symbiont-mediated perturbation of host chromatin organization / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions / 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 / ribonucleoside triphosphate phosphatase activity / integrin-mediated signaling pathway / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / picornain 3C / T=pseudo3 icosahedral viral capsid / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / modification-dependent protein catabolic process / ISG15 antiviral mechanism / host cell cytoplasmic vesicle membrane / protein tag activity / positive regulation of type II interferon production / Interferon alpha/beta signaling / integrin binding / regulation of translation / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / molecular adaptor activity / clathrin-dependent endocytosis of virus by host cell / defense response to virus / viral protein processing / RNA helicase activity / host cell endoplasmic reticulum membrane / defense response to bacterium / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / innate immune response / RNA-directed RNA polymerase activity / DNA-templated transcription / ubiquitin protein ligase binding / host cell nucleus / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / proteolysis / RNA binding / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Cysteine proteinases ...: / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Cysteine proteinases / Cathepsin B; Chain A / Picornavirus coat protein / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Ubiquitin domain / Viral coat protein subunit / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSwatek, K.N. / Pruneda, J.N. / Komander, D.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council309756 United Kingdom
European Research Council724804 United Kingdom
Lister Institute for Preventative Medicine United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Irreversible inactivation of ISG15 by a viral leader protease enables alternative infection detection strategies.
Authors: Swatek, K.N. / Aumayr, M. / Pruneda, J.N. / Visser, L.J. / Berryman, S. / Kueck, A.F. / Geurink, P.P. / Ovaa, H. / van Kuppeveld, F.J.M. / Tuthill, T.J. / Skern, T. / Komander, D.
History
DepositionJan 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: 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
Revision 1.4Oct 16, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,61410
Polymers27,8652
Non-polymers7498
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-42 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.188, 40.352, 58.052
Angle α, β, γ (deg.)90.00, 91.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-382-

HOH

21A-400-

HOH

31A-416-

HOH

41A-435-

HOH

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Components

#1: Protein Lbpro


Mass: 19055.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Production host: Escherichia coli (E. coli) / References: UniProt: P03305
#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: 8810.099 Da / Num. of mol.: 1
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2 M Ammonium Sulfate 0.2 M Sodium potassium tartrate tetrahydrate 0.1 M Sodium citrate tribasic (pH 5.6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.5→58.023 Å / Num. obs: 42227 / % possible obs: 99.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2043 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qol

1qol


Resolution: 1.5→58.023 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.1863 2073 4.91 %
Rwork0.1652 --
obs0.1662 42214 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→58.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 45 213 2109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021982
X-RAY DIFFRACTIONf_angle_d1.3392712
X-RAY DIFFRACTIONf_dihedral_angle_d14.7511156
X-RAY DIFFRACTIONf_chiral_restr0.099294
X-RAY DIFFRACTIONf_plane_restr0.01349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53490.29151440.2382610X-RAY DIFFRACTION98
1.5349-1.57330.25681470.22512665X-RAY DIFFRACTION100
1.5733-1.61590.25481350.20432671X-RAY DIFFRACTION99
1.6159-1.66340.21421330.19582659X-RAY DIFFRACTION99
1.6634-1.71710.22871200.1852673X-RAY DIFFRACTION99
1.7171-1.77850.22221470.17392650X-RAY DIFFRACTION99
1.7785-1.84970.20871170.1722683X-RAY DIFFRACTION99
1.8497-1.93390.17421510.16472660X-RAY DIFFRACTION98
1.9339-2.03580.23631060.16242696X-RAY DIFFRACTION100
2.0358-2.16340.19171510.15642664X-RAY DIFFRACTION100
2.1634-2.33040.16991360.16422686X-RAY DIFFRACTION99
2.3304-2.5650.1711450.16332647X-RAY DIFFRACTION99
2.565-2.93610.1871560.1722680X-RAY DIFFRACTION98
2.9361-3.69910.16081400.15772721X-RAY DIFFRACTION100
3.6991-58.06630.17131450.14842776X-RAY DIFFRACTION99
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)
12.19570.09410.32330.5661-0.09373.0047-0.0015-0.1273-0.01550.0198-0.0698-0.06970.11430.13690.0620.10980.00590.00840.09190.02250.11968.5763-36.39472.869
27.04162.3651-2.07062.0688-0.60491.72410.2175-0.15340.51380.0291-0.11540.1266-0.12670.1291-0.09520.1561-0.0210.01710.1696-0.00360.160429.3022-20.232771.1506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 29 through 184)
2X-RAY DIFFRACTION2(chain 'B' and resid 78 through 154)

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