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- PDB-5cht: Crystal structure of USP18 -

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Basic information

Entry
Database: PDB / ID: 5cht
TitleCrystal structure of USP18
ComponentsUbl 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 / ISG15 antiviral mechanism / TAK1-dependent IKK and NF-kappa-B activation / Ub-specific processing proteases / negative regulation of type I interferon-mediated signaling pathway / protein deubiquitination / antiviral innate immune response / response to bacterium ...Regulation of IFNA/IFNB signaling / response to stilbenoid / Regulation of NF-kappa B signaling / ISG15 antiviral mechanism / TAK1-dependent IKK and NF-kappa-B activation / Ub-specific processing proteases / negative regulation of type I interferon-mediated signaling pathway / protein deubiquitination / antiviral innate immune response / response to bacterium / ISG15-specific peptidase activity / regulation of inflammatory response / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / 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 / Papain-like cysteine peptidase superfamily ...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 / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubl carboxyl-terminal hydrolase 18
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.0Jun 29, 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.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubl carboxyl-terminal hydrolase 18
B: Ubl carboxyl-terminal hydrolase 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3255
Polymers75,1292
Non-polymers1963
Water99155
1
A: Ubl carboxyl-terminal hydrolase 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6953
Polymers37,5641
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubl carboxyl-terminal hydrolase 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6302
Polymers37,5641
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.959, 89.747, 149.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 37564.258 Da / Num. of mol.: 2 / Fragment: UNP residues 46-368
Source method: isolated from a genetically manipulated source
Details: USP18 was truncated at the N-terminus. Residues 1-45 are missing. Residues 43, 44,45 given in the pdb are originating from the purification tag.
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.09 M succinate, pH 7.0, 13.5% (w/v) PEG 3350, 10 mM KBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→28 Å / Num. obs: 18487 / % possible obs: 99.76 % / Redundancy: 4.86 % / Rmerge(I) obs: 0.301 / Net I/σ(I): 6.29
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.96 % / Rmerge(I) obs: 2.771 / Mean I/σ(I) obs: 0.79 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NB8

1nb8


Resolution: 2.8→27.772 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2829 938 5.07 %
Rwork0.2249 --
obs0.2279 18487 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→27.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4883 0 3 55 4941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095009
X-RAY DIFFRACTIONf_angle_d1.0596774
X-RAY DIFFRACTIONf_dihedral_angle_d15.2851824
X-RAY DIFFRACTIONf_chiral_restr0.055774
X-RAY DIFFRACTIONf_plane_restr0.007843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94750.40841320.38982454X-RAY DIFFRACTION100
2.9475-3.13190.37721190.34592470X-RAY DIFFRACTION100
3.1319-3.37330.37841440.29512468X-RAY DIFFRACTION100
3.3733-3.71210.29421230.23312487X-RAY DIFFRACTION100
3.7121-4.24760.27081270.21222513X-RAY DIFFRACTION100
4.2476-5.34530.22191400.17372527X-RAY DIFFRACTION100
5.3453-27.77290.25691530.18552630X-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)
11.90790.2136-0.05580.34540.49960.5115-0.05660.29340.0614-0.1191-0.10970.1491-0.1350.212-0.13550.33170.056-0.03130.2774-0.02280.288158.312110.209586.7094
20.6001-0.3253-0.51252.08920.50840.52410.14450.37460.07-0.74330.18110.2161-0.2838-0.19690.410.32360.105-0.06850.2079-0.07510.240255.09078.600974.4454
3-0.1033-0.06310.06720.183-0.09170.1328-0.18090.76360.3179-0.04880.19320.260.34560.1815-0.00060.5777-0.0382-0.07820.6798-0.12310.608237.1747-9.06168.7119
40.1074-0.095-0.03760.0740.05710.0064-0.12390.43351.1344-0.4276-0.0713-0.21850.25640.0386-0.00630.8785-0.0626-0.19930.9336-0.32720.744633.2391-13.384754.6132
50.47730.5392-0.56760.5889-0.1070.920.0327-0.0309-0.0890.15460.0457-0.0680.1584-0.16260.26590.32170.0383-0.08630.357-0.12860.378338.26131.333985.395
61.07150.32670.0530.39840.4421.59890.04320.1476-0.3887-0.0357-0.01530.08830.3506-0.01560.11730.2468-0.02820.02570.34560.0410.334323.019526.613198.655
70.6563-0.0995-0.04670.261-0.4860.4902-0.09950.39540.1745-0.1455-0.1540.3543-0.0757-0.4404-0.00910.32110.01220.05330.4185-0.06650.465826.603533.824799.3934
8-0.00810.0277-0.1330.1481-0.15190.2761-0.2555-0.15120.0599-0.16520.3567-0.0916-0.0274-0.1179-00.3194-0.00010.01670.6515-0.06690.32946.464146.4624112.8274
90.093-0.0132-0.02880.03340.01190.11590.1322-0.0572-0.1742-0.5073-0.5062-0.2296-0.17420.3653-0.00210.61730.09810.01880.6256-0.14930.53846.632260.1568110.6123
101.24220.07080.60871.6456-0.04860.35610.01370.12570.00650.06170.0080.07050.03770.0549-0.00020.28410.00260.00340.231-0.02950.208543.035427.1992106.9851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 43:115)
2X-RAY DIFFRACTION2(chain A and resid 116:163)
3X-RAY DIFFRACTION3(chain A and resid 164:213)
4X-RAY DIFFRACTION4(chain A and resid 214:240)
5X-RAY DIFFRACTION5(chain A and resid 241:367)
6X-RAY DIFFRACTION6(chain B and resid 48:106)
7X-RAY DIFFRACTION7(chain B and resid 107:171)
8X-RAY DIFFRACTION8(chain B and resid 172:213)
9X-RAY DIFFRACTION9(chain B and resid 214:239)
10X-RAY DIFFRACTION10(chain B and resid 240:366)

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