[English] 日本語
Yorodumi
- PDB-6ffa: FMDV Leader protease bound to substrate ISG15 -

+
Open data


ID or keywords:

Loading...

-
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


positive regulation of protein oligomerization / L-peptidase / ISG15-protein conjugation / regulation of type II interferon production / suppression by virus of host type I interferon production / modulation by virus of host chromatin organization / protein localization to mitochondrion / NS1 Mediated Effects on Host Pathways / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway ...positive regulation of protein oligomerization / L-peptidase / ISG15-protein conjugation / regulation of type II interferon production / suppression by virus of host type I interferon production / modulation by virus of host chromatin organization / protein localization to mitochondrion / NS1 Mediated Effects on Host Pathways / 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 / ribonucleoside triphosphate phosphatase activity / picornain 3C / positive regulation of erythrocyte differentiation / T=pseudo3 icosahedral viral capsid / integrin-mediated signaling pathway / Negative regulators of DDX58/IFIH1 signaling / host cell cytoplasmic vesicle membrane / Termination of translesion DNA synthesis / response to virus / modification-dependent protein catabolic process / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / protein tag activity / ISG15 antiviral mechanism / : / Interferon alpha/beta signaling / positive regulation of type II interferon production / integrin binding / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / defense response to virus / RNA helicase activity / molecular adaptor activity / host cell endoplasmic reticulum membrane / viral protein processing / defense response to bacterium / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / innate immune response / 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 / membrane / cytosol / cytoplasm
Similarity search - Function
: / Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 ...: / Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Ubiquitin domain / Viral coat protein subunit / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / 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. / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Glycerol


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more