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- PDB-9nn9: ISG15 complexed with nanobody -

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Basic information

Entry
Database: PDB / ID: 9nn9
TitleISG15 complexed with nanobody
Components
  • Nanobody
  • Ubiquitin-like protein ISG15
KeywordsIMMUNE SYSTEM / Ubiquitin-like
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 / Negative regulators of DDX58/IFIH1 signaling / positive regulation of erythrocyte differentiation / Termination of translesion DNA synthesis / integrin-mediated signaling pathway / DDX58/IFIH1-mediated induction of interferon-alpha/beta / modification-dependent protein catabolic process / ISG15 antiviral mechanism / protein tag activity / PKR-mediated signaling / response to virus / Interferon alpha/beta signaling / integrin binding / positive regulation of type II interferon production / 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
: / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesHomo sapiens (human)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsDabhade, P. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM141834 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Identification and characterization of nanobodies specific for the human ubiquitin-like ISG15 protein.
Authors: Gan, J. / Dabhade, P. / Wijne, C. / McKibben, W. / Draganov, S.D. / Alrawili, H. / Sun, Z.J. / Houghton, J.W. / Tate, E.W. / Le Gall, C. / Suresh, P. / Pishesha, N. / Pinto-Fernandez, A. / ...Authors: Gan, J. / Dabhade, P. / Wijne, C. / McKibben, W. / Draganov, S.D. / Alrawili, H. / Sun, Z.J. / Houghton, J.W. / Tate, E.W. / Le Gall, C. / Suresh, P. / Pishesha, N. / Pinto-Fernandez, A. / Schwartz, T.U. / Ploegh, H.L.
History
DepositionMar 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-like protein ISG15
B: Nanobody
C: Ubiquitin-like protein ISG15
D: Nanobody
E: Ubiquitin-like protein ISG15
F: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,68810
Polymers103,4066
Non-polymers2824
Water2,846158
1
A: Ubiquitin-like protein ISG15
B: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6274
Polymers34,4692
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin-like protein ISG15
D: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5313
Polymers34,4692
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ubiquitin-like protein ISG15
F: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5313
Polymers34,4692
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.460, 114.470, 79.290
Angle α, β, γ (deg.)90.00, 105.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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: 18150.676 Da / Num. of mol.: 3 / Fragment: residues 1-157 / 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
#2: Antibody Nanobody


Mass: 16317.908 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 25 % PEG 3350, 0.1 M trisodium citrate pH 5.6, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.59→99 Å / Num. obs: 36396 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1343 / Rpim(I) all: 0.085 / Rrim(I) all: 0.1593 / Net I/σ(I): 6.91
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.8263 / Mean I/σ(I) obs: 1.26 / Num. unique obs: 2168 / CC1/2: 0.344 / CC star: 0.716 / Rpim(I) all: 0.5274 / Rrim(I) all: 0.9829 / % possible all: 95.69

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XSCALEVERSION Jun 30, 2024 BUILT=20241002data scaling
XDSVERSION Jun 30, 2024 BUILT=20241002data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→76.27 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2443 2272 6.24 %
Rwork0.188 --
obs0.1915 36382 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→76.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6330 0 17 158 6505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096474
X-RAY DIFFRACTIONf_angle_d1.0398772
X-RAY DIFFRACTIONf_dihedral_angle_d18.7532349
X-RAY DIFFRACTIONf_chiral_restr0.055988
X-RAY DIFFRACTIONf_plane_restr0.0081120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.650.32421380.28612062X-RAY DIFFRACTION96
2.65-2.710.33951410.28242121X-RAY DIFFRACTION100
2.71-2.780.33991410.26012132X-RAY DIFFRACTION100
2.78-2.850.31751440.24222146X-RAY DIFFRACTION100
2.85-2.940.31131420.23012135X-RAY DIFFRACTION100
2.94-3.030.29361440.22732131X-RAY DIFFRACTION100
3.03-3.140.251410.212117X-RAY DIFFRACTION100
3.14-3.260.28241430.20262159X-RAY DIFFRACTION100
3.26-3.410.29181410.19762118X-RAY DIFFRACTION100
3.41-3.590.26981440.19352151X-RAY DIFFRACTION100
3.59-3.820.23971410.17622126X-RAY DIFFRACTION99
3.82-4.110.21881390.15872106X-RAY DIFFRACTION99
4.11-4.530.20611410.14882139X-RAY DIFFRACTION99
4.53-5.180.18991430.14792138X-RAY DIFFRACTION99
5.18-6.530.20861440.18152150X-RAY DIFFRACTION100
6.53-76.270.22351450.18482179X-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)
11.3134-0.08670.1636.1655-1.94881.76650.12820.1053-0.0812-0.2843-0.10770.23630.16020.0285-0.00970.27890.0138-0.00480.3613-0.05110.27425.4327-53.252829.163
22.3771.01210.74224.1390.01051.4147-0.0244-0.00280.17330.1065-0.1157-0.04990.0309-0.04160.13070.3093-0.01230.0050.3295-0.02060.345415.5359-24.985637.9167
34.10462.0636-1.83752.6157-1.15251.74310.0729-0.35240.11810.1746-0.2214-0.1239-0.23180.26680.17180.532-0.0171-0.0670.42260.00010.323130.4319.99771.4572
42.3998-0.20630.22882.29361.7582.7402-0.0535-0.2037-0.21930.1883-0.01920.17930.038-0.06830.04940.5512-0.04670.09890.4170.02120.411416.2259-17.149462.4527
53.04531.37291.77252.79462.00183.1546-0.0834-0.0273-0.1369-0.03380.0516-0.2672-0.10960.13510.00130.32610.00070.04630.31650.07460.31615.3101-54.260156.9551
65.36590.39551.08782.7049-0.32612.3756-0.0091-0.46420.25620.043-0.06410.3596-0.0184-0.13750.10680.26270.00040.0040.3501-0.06970.3808-25.5893-56.670452.7863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'

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