9LW4 | pdb_00009lw4

UbCh8-ISG15 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.269 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.233 (DCC) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9LW4

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

ISGylation mechanism uncovers conformational specificity for HECT-family E3 ligase HERC5.

Sahoo, P.Parmar, G.G.Lenka, D.R.Sherawat, M.Trivedi, B.S.Kumar, A.

(2026) Cell Rep 45: 117565-117565

  • DOI: https://doi.org/10.1016/j.celrep.2026.117565
  • Primary Citation Related Structures: 
    9LW4

  • PubMed Abstract: 

    Interferon-stimulated gene 15 (ISG15), composed of two ubiquitin-like domains, plays a critical role in antiviral immunity. Although the ubiquitination mechanism is well established, the mechanisms governing ISG15 transfer, particularly from E2 to E3 and subsequent lysine conjugation, remain unknown. Here, we reveal that UbcH8(E2)∼ISG15 exhibits striking specificity for HECT-family E3 ligases (particularly HERC5) but is inactive with RING or RBR E3. In contrast, UbcH8∼Ub preferentially engages RBR E3, indicating a switched E2-E3 specificity depending on the conjugated ubiquitin-like modifier. Structural and biochemical studies uncover how a closed conformation of UbcH8∼ISG15 enables trans-thiolation mediated by selective HECT-family E3 ligases. We further demonstrate that HERC5's C-lobe specifically recognizes donor ISG15 for lysine conjugation, explaining its exclusive ISGylation activity and lack of ubiquitination function. These findings delineate the molecular basis of ISG15 conjugation and reveal how its pathway has evolved distinct mechanisms from ubiquitination, offering new avenues for therapeutic intervention.


  • Organizational Affiliation
    • Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal 462066, India.

Macromolecule Content 

  • Total Structure Weight: 52.97 kDa 
  • Atom Count: 3,891 
  • Modeled Residue Count: 456 
  • Deposited Residue Count: 456 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin/ISG15-conjugating enzyme E2 L6A [auth B],
C
152Homo sapiensMutation(s): 0 
Gene Names: UBE2L6UBCH8
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for O14933 (Homo sapiens)
Explore O14933 
Go to UniProtKB:  O14933
PHAROS:  O14933
GTEx:  ENSG00000156587 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14933
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ubiquitin-like protein ISG15B [auth A],
D
76Homo sapiensMutation(s): 0 
Gene Names: ISG15G1P2UCRP
UniProt & NIH Common Fund Data Resources
Find proteins for P05161 (Homo sapiens)
Explore P05161 
Go to UniProtKB:  P05161
PHAROS:  P05161
GTEx:  ENSG00000187608 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05161
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
L [auth D]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
3CN
(Subject of Investigation/LOI)

Query on 3CN



Download:Ideal Coordinates CCD File
F [auth A],
M [auth D]
3-AMINOPROPANE
C3 H9 N
WGYKZJWCGVVSQN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth B]
H [auth A]
I [auth C]
J [auth C]
K [auth C]
E [auth B],
H [auth A],
I [auth C],
J [auth C],
K [auth C],
N [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.269 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.233 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.984α = 90
b = 32.313β = 93.607
c = 107.042γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)India--
Other governmentIndiaIISER Bhopal MHRD

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-01
    Type: Initial release