[English] 日本語
Yorodumi
- PDB-5jze: Erve virus viral OTU domain protease in complex with mouse ISG15 -

+
Open data


ID or keywords:

Loading...

-
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 / polyubiquitin modification-dependent protein binding / 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 / protein tag activity / positive regulation of type II interferon production / integrin binding / ubiquitin-dependent protein catabolic process / 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 / cytosol
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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...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 / Replicase / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Allylamine


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


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


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.46 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

-
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

-
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 %

+
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