[English] 日本語
Yorodumi
- PDB-5chv: Crystal structure of USP18-ISG15 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5chv
TitleCrystal structure of USP18-ISG15 complex
Components
  • Ubiquitin-like protein ISG15
  • Ubl carboxyl-terminal hydrolase 18
KeywordsHYDROLASE / Ubiquitin-specific protease / ISG15 / interferon
Function / homology
Function and homology information


Regulation of IFNA/IFNB signaling / response to stilbenoid / Regulation of NF-kappa B signaling / 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 / TAK1-dependent IKK and NF-kappa-B activation ...Regulation of IFNA/IFNB signaling / response to stilbenoid / Regulation of NF-kappa B signaling / 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 / TAK1-dependent IKK and NF-kappa-B activation / protein localization to mitochondrion / Ub-specific processing proteases / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / protein deubiquitination / antiviral innate immune response / 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 / ISG15-specific peptidase activity / regulation of inflammatory response / ubiquitin-dependent protein catabolic process / defense response to virus / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / defense response to bacterium / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / extracellular region / nucleus / cytosol
Similarity search - Function
: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Cathepsin B; Chain A ...: / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / 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
Ubiquitin-like protein ISG15 / Ubl carboxyl-terminal hydrolase 18
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.005 Å
AuthorsFritz, G. / Basters, A.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural basis of the specificity of USP18 toward ISG15.
Authors: Basters, A. / Geurink, P.P. / Rocker, A. / Witting, K.F. / Tadayon, R. / Hess, S. / Semrau, M.S. / Storici, P. / Ovaa, H. / Knobeloch, K.P. / Fritz, G.
History
DepositionJul 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Mar 15, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: 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.conn_type_id / _struct_conn.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_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
A: Ubl carboxyl-terminal hydrolase 18
C: Ubiquitin-like protein ISG15
B: Ubl carboxyl-terminal hydrolase 18
D: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,80810
Polymers109,4144
Non-polymers3946
Water905
1
A: Ubl carboxyl-terminal hydrolase 18
C: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9045
Polymers54,7072
Non-polymers1973
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-46 kcal/mol
Surface area20920 Å2
MethodPISA
2
B: Ubl carboxyl-terminal hydrolase 18
D: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9045
Polymers54,7072
Non-polymers1973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-39 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.040, 72.806, 217.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Ubl carboxyl-terminal hydrolase 18 / 43 kDa ISG15-specific protease / ISG15-specific-processing protease / Ubl thioesterase 18


Mass: 37353.039 Da / Num. of mol.: 2 / Fragment: UNP residues 46-368
Source method: isolated from a genetically manipulated source
Details: The protein was expressed without the N-terminal 45 residues. The construct contains residues 46-368 out of 368 residues.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Usp18, Ubp43 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WTV6, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#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


Mass: 17354.049 Da / Num. of mol.: 2 / Fragment: UNP residues 1-155
Source method: isolated from a genetically manipulated source
Details: In ISG15 chain C the terminal Glycine 155 is replaced by a propargylamine that reacts with the active site Cysteine 61 of USP18 chain A and forms a covalent bond.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Isg15, G1p2, Ucrp / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q64339

-
Non-polymers , 4 types, 11 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.12 Å3/Da / Density % sol: 42.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.1 M MOPS/Hepes-NaOH, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→37 Å / Num. obs: 21117 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 56.58 Å2 / Rmerge F obs: 0.971 / Rmerge(I) obs: 0.627 / Rrim(I) all: 0.653 / Χ2: 0.413 / Net I/σ(I): 3.53 / Num. measured all: 274828
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3-3.160.3482.9340.8638885300130013.054100
3.16-3.50.6051.6971.5661508468746861.766100
3.5-40.860.8742.9159096433443330.908100
4-60.960.4225.0680427628862880.44100
6-100.9840.2796.5327976216621660.29100
100.9920.1589.2869366576430.16697.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CHT, 5CHF

5cht

5chf


Resolution: 3.005→37.312 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2862 1020 4.87 %
Rwork0.2247 --
obs0.2277 20936 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.005→37.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7339 0 14 5 7358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087500
X-RAY DIFFRACTIONf_angle_d1.2310149
X-RAY DIFFRACTIONf_dihedral_angle_d16.6852789
X-RAY DIFFRACTIONf_chiral_restr0.0551159
X-RAY DIFFRACTIONf_plane_restr0.0071271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.005-3.16340.36921410.32642748X-RAY DIFFRACTION98
3.1634-3.36150.34991480.28462801X-RAY DIFFRACTION100
3.3615-3.62080.33591410.24992800X-RAY DIFFRACTION100
3.6208-3.98480.2941510.22362819X-RAY DIFFRACTION100
3.9848-4.56050.26781470.20092849X-RAY DIFFRACTION100
4.5605-5.74240.24791330.19492883X-RAY DIFFRACTION100
5.7424-37.31480.25381590.20113016X-RAY DIFFRACTION100

+
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