RNF8 E3 Ubiquitin Ligase Stimulates Ubc13 E2 Conjugating Activity That Is Essential for DNA Double Strand Break Signaling and BRCA1 Tumor Suppressor Recruitment.

Hodge CD, Ismail IH, Edwards RA, Hura GL, Xiao AT, Tainer JA, Hendzel MJ, Glover JN, J Biol Chem 291(18):9396-410 (2016) Europe PMC

SASDBS3 – Wild type RNF8 complexed with Ubc13 (C87K, K92A mutant) and Mms2: conjugated to Ubiquitin

E3 ubiquitin-protein ligase RNF8
Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A)
Polyubiquitin-C
Ubiquitin-conjugating enzyme E2 variant 2
MWexperimental 107 kDa
MWexpected 122 kDa
VPorod 214 nm3
log I(s) 1.27×103 1.27×102 1.27×101 1.27×100
E3 ubiquitin-protein ligase RNF8 Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) Polyubiquitin-C Ubiquitin-conjugating enzyme E2 variant 2 small angle scattering data  s, nm-1
ln I(s)
E3 ubiquitin-protein ligase RNF8 Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) Polyubiquitin-C Ubiquitin-conjugating enzyme E2 variant 2 Guinier plot ln 1.28×103 Rg: 5.4 nm 0 (5.4 nm)-2 s2
(sRg)2I(s)/I(0)
E3 ubiquitin-protein ligase RNF8 Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) Polyubiquitin-C Ubiquitin-conjugating enzyme E2 variant 2 Kratky plot 1.104 0 3 sRg
p(r)
E3 ubiquitin-protein ligase RNF8 Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) Polyubiquitin-C Ubiquitin-conjugating enzyme E2 variant 2 pair distance distribution function Rg: 5.7 nm 0 Dmax: 23.8 nm

Data validation


Fits and models


log I(s)
 s, nm-1
E3 ubiquitin-protein ligase RNF8 Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) Polyubiquitin-C Ubiquitin-conjugating enzyme E2 variant 2 MES-FOXS model
E3 ubiquitin-protein ligase RNF8 Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) Polyubiquitin-C Ubiquitin-conjugating enzyme E2 variant 2 MES-FOXS model
E3 ubiquitin-protein ligase RNF8 Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) Polyubiquitin-C Ubiquitin-conjugating enzyme E2 variant 2 MES-FOXS model
E3 ubiquitin-protein ligase RNF8 Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) Polyubiquitin-C Ubiquitin-conjugating enzyme E2 variant 2 MES-FOXS model
E3 ubiquitin-protein ligase RNF8 Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) Polyubiquitin-C Ubiquitin-conjugating enzyme E2 variant 2 MES-FOXS model

X-ray synchrotron radiation scattering data from solutions of a 2:2:2:2 complex of E3 ubiquitin-protein ligase RNF8, Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A), Ubiquitin-conjugating enzyme E2 variant 2 and Polyubiquitin-C in 20 mM HEPES 200 mM NaCl, 0.01 mM, ZnSO4, and 1 mM DTT were collected on the BL12.3.1 SIBYLS camera on the storage ring ALS (Berkeley, CA, USA) using a Pilatus 2M detector (s = 4π sin θ/λ, where 2θ is the scattering angle). The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the curves were scaled for protein concentration. The models shown in this entry were generated in BILBOMD from an initial pool of 7195 structures. The theoretical scattering profiles for those models were calculated using FoXS, and FoXS was also used to run a minimal ensemble search (MES). The percent contribution to the MES is written in the header of each of the PDB file, expressed as a volume fraction. For the models displayed in this entry, the volume-fractions are (from top to bottom): 0.42, 0.35, 0.15, 0.04 and 0.03. The fit of the MES was calculated using FoXS.

Cell temperature = UNKNOWN. Storage temperature = UNKNOWN. Sample detector distance = UNKNOWN. X-ray Exposure time = UNKNOWN. Number of frames = UNKNOWN. Concentration = UNKNOWN

E3 ubiquitin-protein ligase RNF8 (RNF8)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   17.6 kDa
 
UniProt   O76064 (345-485)
Sequence   FASTA
 
Ubiquitin-conjugating enzyme E2 N double mutant (C87K, K92A) (Ubc13 - C87K, K92A)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   17.9 kDa
 
UniProt   P61088 (1-152)
Sequence   FASTA
 
Polyubiquitin-C (UBC)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   8.6 kDa
 
UniProt   P0CG48 (1-76)
Sequence   FASTA
 
Ubiquitin-conjugating enzyme E2 variant 2 (Mms2 (UBE2V2))
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   17.1 kDa
 
UniProt   Q15819 (1-145)
Sequence   FASTA