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- PDB-1z2m: Crystal Structure of ISG15, the Interferon-Induced Ubiquitin Cros... -

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Basic information

Entry
Database: PDB / ID: 1z2m
TitleCrystal Structure of ISG15, the Interferon-Induced Ubiquitin Cross Reactive Protein
Componentsinterferon, alpha-inducible protein (clone IFI-15K)
KeywordsSIGNALING PROTEIN / ISG15 / Ubiquitin Cross Reactive Protein
Function / homology
Function and homology information


ISG15-protein conjugation / positive regulation of protein oligomerization / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / 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 ...ISG15-protein conjugation / positive regulation of protein oligomerization / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / 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 / 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 / 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 / defense response to virus / defense response to bacterium / innate immune response / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIR / Resolution: 2.5 Å
AuthorsNarasimhan, J. / Wang, M. / Fu, Z. / Klein, J.M. / Haas, A.L. / Kim, J.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of the Interferon-induced Ubiquitin-like Protein ISG15.
Authors: Narasimhan, J. / Wang, M. / Fu, Z. / Klein, J.M. / Haas, A.L. / Kim, J.J.
History
DepositionMar 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: interferon, alpha-inducible protein (clone IFI-15K)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2242
Polymers17,0341
Non-polymers1901
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.790, 56.940, 103.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein interferon, alpha-inducible protein (clone IFI-15K) / ISG15


Mass: 17033.535 Da / Num. of mol.: 1 / Mutation: c78s
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pED11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05161
#2: Chemical ChemComp-OS4 / OSMIUM 4+ ION


Mass: 190.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Os
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris-HCl buffer, PEG4K, MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 18, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→29.55 Å / Num. all: 5624 / Num. obs: 5624 / % possible obs: 93.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.06 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 511 / Rsym value: 0.192 / % possible all: 88.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: SIR / Resolution: 2.5→29.55 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 142510.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.223 603 10.7 %RANDOM
Rwork0.206 ---
obs0.206 5624 93.9 %-
all-5624 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.9459 Å2 / ksol: 0.37215 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1173 0 1 39 1213
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.312.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.336 57 11.2 %
Rwork0.291 454 -
obs-511 88.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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