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- PDB-2hj8: Solution NMR structure of the C-terminal domain of the interferon... -

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Basic information

Entry
Database: PDB / ID: 2hj8
TitleSolution NMR structure of the C-terminal domain of the interferon alpha-inducible ISG15 protein from Homo sapiens. Northeast Structural Genomics target HR2873B
ComponentsInterferon-induced 17 kDa protein
KeywordsSIGNALING PROTEIN / HR2873B / human ISG15 / Northeast Structural Genomics Consortium / Protein Structure Initiative / NESG / PSI-1
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)
MethodSOLUTION NMR / simulated annealing
AuthorsAramini, J.M. / Ho, C.K. / Yin, C. / Cunningham, K. / Janjua, H. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the C-terminal domain of the interferon alpha-inducible ISG15 protein from Homo sapiens. Northeast Structural Genomics target HR2873B.
Authors: Aramini, J.M. / Ho, C.K. / Yin, C. / Cunningham, K. / Janjua, H. / Li, M.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999 SEQUENCE The author states that the sequence numbering is +7 relative to the numbering in the ... SEQUENCE The author states that the sequence numbering is +7 relative to the numbering in the native protein, to be consistent with ongoing work on the full length human ISG15 protein in their laboratory.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-induced 17 kDa protein


Theoretical massNumber of molelcules
Total (without water)10,1131
Polymers10,1131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with lowest conformational energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Interferon-induced 17 kDa protein / hUCRP / Interferon-induced 15 kDa protein


Mass: 10113.471 Da / Num. of mol.: 1
Fragment: ISG15 C-terminal domain (8.9 kDa), Ubiquitin-like 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Plasmid: HR2873B-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: P05161

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
142high resolution 2D CH-HSQC (for stereospecific assignment of Val/Leu methyls)
1512D 15N,1H heteronuclear NOE
1613D TR backbone expts
1713D (H)CCH-COSY, 3D (H)CCH-TOCSYs
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. ...Text: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS AS WELL AS DISTANCE AND HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING AUTOSTRUCTURE. DIHEDRAL ANGLE CONSTRAINTS WERE DETERMINED USING HYPER. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING N-TERMINAL MET AND C-TERMINAL HHHHHH): BACKBONE, 99.8%, SIDE CHAIN, 95.3%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 95.2%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 86 TO 160, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE 89-94,100-108,111-124,126-132,135-136,139-158: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 86.7%, ADDITIONALLY ALLOWED, 12.7%, GENEROUSLY ALLOWED, 0.6%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.60/-2.05, ALL, -0.44/-2.60. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 28.41/-3.35. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (ALL RESIDUES): RECALL, 0.978, PRECISION, 0.910, F-MEASURE, 0.943, DP-SCORE, 0.811.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.81 mM U-13C,15N HR2873B, 50 mM ammonium citrate, 5 mM CaCl2, 1x protease inhibitor, 0.02% NaN3, pH 6.5, 5% D2O / 95% H2O5% D2O / 95% H2O
20.9 mM 5%-13C,U-15N HR2873B, 50 mM ammonium citrate, 5 mM CaCl2, 1x protease inhibitor, 0.02% NaN3, pH 6.5, 5% D2O / 95% H2O5% D2O / 95% H2O
Sample conditionsIonic strength: 50 mM ammonium citrate, 5 mM CaCl2 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5pl6Brukercollection
VNMR6.1CVariancollection
AutoAssign2.2.1Zimmerman, Moseley, Montelionedata analysis
Sparky3.11Goddard & Knellerdata analysis
AutoStructure2.1.1Huang & Montelionerefinement
XPLOR-NIH2.11.2Clore et alrefinement
NMRPipe2.3Delaglio et alprocessing
PdbStat4.1Tejero & Montelionedata analysis
PSVS1.3Bhattacharya, Hang, Montelionedata analysis
CNS1.1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 976 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 80 DIHEDRAL ANGLE CONSTRAINTS, AND 40 HYDROGEN BOND CONSTRAINTS (14.6 CONSTRAINTS ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 976 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 80 DIHEDRAL ANGLE CONSTRAINTS, AND 40 HYDROGEN BOND CONSTRAINTS (14.6 CONSTRAINTS PER RESIDUE, 4.8 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 86 to 160 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING AUTOSTRUCTURE (XPLOR-NIH). AFTER A FINAL XPLOR CALCULATION USING THE CONSTRAINTS DERIVED FROM AUTOSTRUCTURE, THE 20 LOWEST ENERGY STRUCTURES OUT OF 100 WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYANMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS). THE N-TERMINAL MET AND UNSTRUCTURED C-TERMINUS OF THE PROTEIN (LRGG + LEHHHHHH TAG) WERE INCLUDED IN ALL STRUCTURE CALCULATIONS BUT HAVE BEEN OMITTED FROM THIS DEPOSITION.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with lowest conformational energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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