[English] 日本語
Yorodumi
- PDB-3pse: Structure of a viral OTU domain protease bound to interferon-stim... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / modification-dependent protein catabolic process / ISG15 antiviral mechanism / positive regulation of type II interferon production / protein tag activity / Interferon alpha/beta signaling / integrin binding / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / defense response to virus / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on ester bonds / 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 / RNA-directed RNA polymerase activity / nucleotide binding / DNA-templated transcription / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular region / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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)

+
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