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- PDB-9lw4: UbCh8-ISG15 complex -

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Basic information

Entry
Database: PDB / ID: 9lw4
TitleUbCh8-ISG15 complex
Components
  • Ubiquitin-like protein ISG15
  • Ubiquitin/ISG15-conjugating enzyme E2 L6
KeywordsIMMUNE SYSTEM / ISG15 conjugation.
Function / homology
Function and homology information


ISG15 transferase activity / positive regulation of protein oligomerization / ISG15-protein conjugation / 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 ...ISG15 transferase activity / positive regulation of protein oligomerization / ISG15-protein conjugation / 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 / E2 ubiquitin-conjugating enzyme / RSV-host interactions / ubiquitin conjugating enzyme activity / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of erythrocyte differentiation / positive regulation of interferon-beta production / protein modification process / integrin-mediated signaling pathway / ubiquitin binding / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / integrin binding / modification-dependent protein catabolic process / positive regulation of type II interferon production / ISG15 antiviral mechanism / response to virus / protein tag activity / protein polyubiquitination / ubiquitin-protein transferase activity / Interferon alpha/beta signaling / Antigen processing: Ubiquitination & Proteasome degradation / defense response to virus / ubiquitin-dependent protein catabolic process / defense response to bacterium / Amyloid fiber formation / innate immune response / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin domain ...: / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
3-AMINOPROPANE / DI(HYDROXYETHYL)ETHER / Ubiquitin/ISG15-conjugating enzyme E2 L6 / Ubiquitin-like protein ISG15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsParmar, G. / Kumar, A.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
Other governmentIISER Bhopal MHRD India
CitationJournal: Cell Rep / Year: 2026
Title: ISGylation mechanism uncovers conformational specificity for HECT-family E3 ligase HERC5.
Authors: Sahoo, P. / Parmar, G.G. / Lenka, D.R. / Sherawat, M. / Trivedi, B.S. / Kumar, A.
History
DepositionFeb 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ubiquitin/ISG15-conjugating enzyme E2 L6
A: Ubiquitin-like protein ISG15
C: Ubiquitin/ISG15-conjugating enzyme E2 L6
D: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,97414
Polymers52,4744
Non-polymers49910
Water3,297183
1
B: Ubiquitin/ISG15-conjugating enzyme E2 L6
A: Ubiquitin-like protein ISG15
C: Ubiquitin/ISG15-conjugating enzyme E2 L6
D: Ubiquitin-like protein ISG15
hetero molecules

B: Ubiquitin/ISG15-conjugating enzyme E2 L6
A: Ubiquitin-like protein ISG15
C: Ubiquitin/ISG15-conjugating enzyme E2 L6
D: Ubiquitin-like protein ISG15
hetero molecules

B: Ubiquitin/ISG15-conjugating enzyme E2 L6
A: Ubiquitin-like protein ISG15
C: Ubiquitin/ISG15-conjugating enzyme E2 L6
D: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,92142
Polymers157,42312
Non-polymers1,49730
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2_555-x,y,-z1
point symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)171.984, 32.313, 107.042
Angle α, β, γ (deg.)90, 93.607, 90
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules BCAD

#1: Protein Ubiquitin/ISG15-conjugating enzyme E2 L6 / E2 ubiquitin-conjugating enzyme L6 / Retinoic acid-induced gene B protein / RIG-B / UbcH8 / ...E2 ubiquitin-conjugating enzyme L6 / Retinoic acid-induced gene B protein / RIG-B / UbcH8 / Ubiquitin carrier protein L6 / Ubiquitin-protein ligase L6


Mass: 17627.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L6, UBCH8 / Production host: Escherichia coli (E. coli)
References: UniProt: O14933, E2 ubiquitin-conjugating enzyme
#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 / hUCRP


Mass: 8609.868 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 193 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-3CN / 3-AMINOPROPANE


Mass: 59.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9N / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5 and 15% w/v PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.6→85.82 Å / Num. obs: 18182 / % possible obs: 97.7 % / Redundancy: 2.8 % / CC1/2: 0.994 / Net I/σ(I): 5.8
Reflection shellResolution: 2.6→9 Å / Num. unique obs: 2196 / CC1/2: 0.884

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Processing

Software
NameVersionClassification
REFMAC5.8.0431 (refmacat 0.4.126)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→65.025 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.219 / SU B: 14.587 / SU ML: 0.286 / Average fsc free: 0.9509 / Average fsc work: 0.9664 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 794 4.89 %RANDOM
Rwork0.2322 15443 --
all0.234 ---
obs-16237 96.799 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.953 Å2
Baniso -1Baniso -2Baniso -3
1--2.003 Å2-0 Å2-0.241 Å2
2---0.136 Å2-0 Å2
3---2.153 Å2
Refinement stepCycle: LAST / Resolution: 2.7→65.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 21 183 3876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123795
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.8485157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.145526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11510655
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.34610175
X-RAY DIFFRACTIONr_chiral_restr0.0980.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022884
X-RAY DIFFRACTIONr_nbd_refined0.2180.21719
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22516
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2186
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.2145
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.217
X-RAY DIFFRACTIONr_mcbond_it1.9613.1071826
X-RAY DIFFRACTIONr_mcangle_it3.3055.5762277
X-RAY DIFFRACTIONr_scbond_it2.7593.4011969
X-RAY DIFFRACTIONr_scangle_it4.5546.0822877
X-RAY DIFFRACTIONr_lrange_it7.83735.4255670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.7-2.770.447450.31611160.32112020.8880.93896.5890.297
2.77-2.8460.304600.31311090.31311880.9380.9498.40070.295
2.846-2.9280.315580.28910990.2911750.940.9598.46810.27
2.928-3.0180.279510.28110300.28111180.9470.95296.69050.257
3.018-3.1170.321560.2559900.25910860.940.96496.31680.235
3.117-3.2260.334570.2399980.24410710.9450.96898.50610.22
3.226-3.3470.334560.2529200.2569940.9290.96598.18910.233
3.347-3.4840.29440.2369210.2389850.9480.96897.96950.218
3.484-3.6380.286480.2249060.2279740.9480.97397.94660.209
3.638-3.8150.217390.2198150.2198750.9710.97797.60.205
3.815-4.0210.271390.2258180.2278830.9640.97797.05550.215
4.021-4.2640.178330.2187490.2158070.9780.97996.90210.209
4.264-4.5570.248390.2027210.2047830.9670.98297.06260.199
4.557-4.920.222310.196500.1927180.9790.98494.84680.191
4.92-5.3860.241350.2066200.2086930.9720.97994.51660.202
5.386-6.0170.225330.2215250.2215870.970.97995.05960.215
6.017-6.9380.27250.2094900.2125470.9740.98394.14990.201
6.938-8.4730.219220.1994290.24760.980.98394.74790.195
8.473-11.8820.214180.173340.1713760.980.98893.6170.189
11.882-65.0250.23950.2272030.2282330.9810.97889.27040.255

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