9LAF | pdb_00009laf

Crystal structure of Elongin BC-EPOP peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 
    0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Literature

Structural analysis of EPOP BC-box binding to the elongin BC complex.

Kim, S.Yeo, H.Lee, B.I.

(2025) Biochem Biophys Res Commun 759: 151691-151691

  • DOI: https://doi.org/10.1016/j.bbrc.2025.151691
  • Primary Citation Related Structures: 
    9LAF

  • PubMed Abstract: 

    The elongin BC complex (ELOBC) interacts with BC-box-containing proteins and plays a role in various cellular processes, including transcriptional regulation and ubiquitination. Elongin BC and polycomb repressive complex 2-associated protein (EPOP) contains a BC-box motif in its N-terminal region and influences cancer cell proliferation and differentiation. A previous study showed that a BC-box containing an EPOP-derived peptide suppresses cancer cell growth and induces apoptosis by disrupting the interaction between the ELOBC and its partner proteins. Here, we report the crystal structure of the EPOP BC-box peptide bound to the ELOBC and compare it with the structures of other BC-box-containing proteins in complex with the ELOBC. The overall structure of interactions between the BC-box and the ELOC was similar across different complexes, indicating a conserved binding mode. Our structural analysis revealed that the strictly conserved leucine residue (Leu40) within the BC-box of EPOP, which was previously suggested to be critical for interactions between the BC-box and the ELOC, was deeply embedded in the hydrophobic pocket of the ELOC protein. This study provided structural insights into BC-box-mediated protein-protein interactions and may serve as a fundamental resource for developing small molecules that modulate the interactions between ELOBC and BC-box-containing proteins.


  • Organizational Affiliation
    • Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea; Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang-si, Gyeonggi-do, 10408, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 25.55 kDa 
  • Atom Count: 1,644 
  • Modeled Residue Count: 195 
  • Deposited Residue Count: 226 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-BA [auth B]104Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens)
Explore Q15370 
Go to UniProtKB:  Q15370
PHAROS:  Q15370
GTEx:  ENSG00000103363 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15370
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-CB [auth C]96Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
Explore Q15369 
Go to UniProtKB:  Q15369
PHAROS:  Q15369
GTEx:  ENSG00000154582 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15369
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin BC and Polycomb repressive complex 2-associated proteinC [auth A]26Homo sapiensMutation(s): 0 
Gene Names: EPOPC17orf96PRR28
UniProt & NIH Common Fund Data Resources
Find proteins for A6NHQ4 (Homo sapiens)
Explore A6NHQ4 
Go to UniProtKB:  A6NHQ4
PHAROS:  A6NHQ4
GTEx:  ENSG00000273604 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6NHQ4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.151α = 90
b = 156.613β = 90
c = 36.817γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government2310200
Other government2510731
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2023-NR076355

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release