3FN1 | pdb_00003fn1

E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification.

• PDB DOI: https://doi.org/10.2210/pdb3FN1/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-12-22 Released: 2009-03-17 
• Deposition Author(s): Huang, D.T., Ayrault, O., Hunt, H.W., Taherbhoy, A.M., Duda, D.M., Scott, D.C., Borg, L.A., Neale, G., Murray, P.J., Roussel, M.F., Schulman, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.265 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

E2-RING expansion of the NEDD8 cascade confers specificity to cullin modification

Huang, D.T., Ayrault, O., Hunt, H.W., Taherbhoy, A.M., Duda, D.M., Scott, D.C., Borg, L.A., Neale, G., Murray, P.J., Roussel, M.F., Schulman, B.A.

(2009) Mol Cell 33: 483-495

• PubMed: 19250909 
• DOI: https://doi.org/10.1016/j.molcel.2009.01.011
• Primary Citation Related Structures: 
  3FN1


• PubMed Abstract: 
  

  Ubiquitin and ubiquitin-like proteins (UBLs) are directed to targets by cascades of E1, E2, and E3 enzymes. The largest ubiquitin E3 subclass consists of cullin-RING ligases (CRLs), which contain one each of several cullins (CUL1, -2, -3, -4, or -5) and RING proteins (RBX1 or -2). CRLs are activated by ligation of the UBL NEDD8 to a conserved cullin lysine. How is cullin NEDD8ylation specificity established? Here we report that, like UBE2M (also known as UBC12), the previously uncharacterized E2 UBE2F is a NEDD8-conjugating enzyme in vitro and in vivo. Biochemical and structural analyses indicate how plasticity of hydrophobic E1-E2 interactions and E1 conformational flexibility allow one E1 to charge multiple E2s. The E2s have distinct functions, with UBE2M/RBX1 and UBE2F/RBX2 displaying different target cullin specificities. Together, these studies reveal the molecular basis for and functional importance of hierarchical expansion of the NEDD8 conjugation system in establishing selective CRL activation.

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Organizational Affiliation: 
• Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.96 kDa 
• Atom Count: 2,127 
• Modeled Residue Count: 252 
• Deposited Residue Count: 265 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD8-activating enzyme E1 catalytic subunit	A	98	Homo sapiens	Mutation(s): 1  Gene Names: E1C, UBA3, UBE1C EC: 6.3.2 (PDB Primary Data), 6.2.1.64 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TBC4 (Homo sapiens) Explore Q8TBC4  Go to UniProtKB:  Q8TBC4
PHAROS:  Q8TBC4 GTEx:  ENSG00000144744

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NEDD8-conjugating enzyme UBE2F	B	167	Homo sapiens	Mutation(s): 0  Gene Names: NCE2, UBE2F EC: 6.3.2 (PDB Primary Data), 2.3.2.34 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q969M7 (Homo sapiens) Explore Q969M7  Go to UniProtKB:  Q969M7
PHAROS:  Q969M7 GTEx:  ENSG00000184182

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.265 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.171	α = 90
b = 81.171	β = 90
c = 212.755	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Huang, D.T., Ayrault, O., Hunt, H.W., Taherbhoy, A.M., Duda, D.M., Scott, D.C., Borg, L.A., Neale, G., Murray, P.J., Roussel, M.F., Schulman, B.A.

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection
• Version 1.6: 2024-10-30
  Changes: Structure summary