2026-08-12 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBe PDBe 2025-07-23 2026-08-12 2026-08-12 2026-08-12 Agence Nationale de la Recherche (ANR) France Structure of the Pyrococcus abyssi 20S proteasome bound to the archaeal activator APA1 Musso F Marino Puertas L Weis F Schoehn G Franzetti B Complex Proteasome Archaea Proteasome activator, PROTEIN BINDING Musso F Marino Puertas L Girard E Gabel F Coute Y Flament D Chenavier F Weis F Schoehn G Franzetti B Structure of the Pyrococcus abyssi 20S proteasome alpha subunit bound to the capping protein APA1 To Be Published 0353 EMD-54520 consensus EM volume
Consensus map of the 20S proteasome from Pyrococcus abyssi in complex with Q9UYJ3 (APA1)
 EMD-54519 focused EM volume
Focused map of Q9UYJ3 (APA1) in complex with the 20S proteasome from Pyrococcus abyssi
 EMD-54518 focused EM volume
Focused map of the 20S proteasome from Pyrococcus abyssi in complex with Q9UYJ3 (APA1)
 9s34 FULLOVERLAP EMDB EMD-54520 consensus EM volume
Consensus map of the 20S proteasome from Pyrococcus abyssi in complex with Q9UYJ3 (APA1)
 EMDB EMD-54519 focused EM volume
Focused map of Q9UYJ3 (APA1) in complex with the 20S proteasome from Pyrococcus abyssi
 EMDB EMD-54518 focused EM volume
Focused map of the 20S proteasome from Pyrococcus abyssi in complex with Q9UYJ3 (APA1)
 EMDB EMD-54521 associated EM volume
Structure of the Pyrococcus abyssi 20S proteasome alpha subunit bound to the capping protein APA1
 20S Proteasome from P. abyssi in complex with the heptameric protein APA1 (Q9UYJ3) 20S Proteasome from P. abyssi in complex with the heptameric protein APA1 (Q9UYJ3) 0 1 2
Assembled 20S core particle reconstituted in vitro from recombinant expression of its three subunit types: alpha, beta-1, beta-2. Beta 2 subunit bears an N-terminal His-tag. Capping protein APA1 sitting on the outer Alpha ring.
Pyrococcus abyssi 20S Proteasome from P. abyssi 1 2 Pyrococcus abyssi 0.711 Archaeal proteasome activator 1 1 1
Heptameric form of the protein, in complex with the proteasome. No tags.
Pyrococcus abyssi 0.234 Archaeal proteasome activator 1 Pyrococcus abyssi 0.03351234399999999 7 Escherichia coli LEVO MKASKLAVKLLKTENDEIIYYDPIYHGRTLKVIGIDDDPALVMEYLLAQYKEKGYNVIVFDTSGKFPTSLFDNILRIEEN SPAGLDPLKLARVGLIKDPYSAVTIIQTIYELDRASTEKLYADFIKGKVNSMDEVVRSKESYAEVINESYTELDEMLFSG EPMKVPESCLIDLSALNSITLTGNAFLILAAMLEDRRSVAYGLYDVSVLTFTDSGNAGLPLITRAARKRVSIVGTRYALD QILNIPGPTLLLYNDPDVQSAIYESQGVPQGFRRFVEKGEGAYIVRSPETIEVEFGMLLR Q9UYJ3 Proteasome subunit alpha Pyrococcus abyssi 0.029035293 7 Escherichia coli LEVO MAFVPPQAGYDRAITVFSPDGRLFQVNYAREAVKRGATAVGVKCKDGVVLAVEKRITSRLIEPESYEKIFQIDDHIAAAS SGIIADARVLVNRARLEAQIHRLTYGEPAPLAVIVKKICDLKQMHTQYGGVRPFGAALLMAGVNDKPELYETDPSGAYFA WKAVAIGSGRNTAMAIFEDKYRDDMTLDEAIKLAIFALAKTMEKPSAENIEVAVITVKDKKFRKLSKEEIEKFLGEVMKE VEEEEVKEKEEDYSELDSHY Q9V122 singleParticle particle 8.0
50 mM Tris pH 8.0, 150 mM NaCl, 150 mM KCl, 10 mM MgCl2
 ETHANE-PROPANE 100 298 FEI VITROBOT MARK IV
SEC-pure form of the 20S
 TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 1.0 2.5 NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1 4835 40.0 1 534489 PHASE FLIPPING AND AMPLITUDE CORRECTION
Reconstruction from Ab-initio volumes generated from 2D projections.
 C7 3.15 FSC 0.143 CUT-OFF cryoSPARC 4.5
50,092 particles aligning to the complex were used for Non Uniform refinement with an imposed C7 symmetry. This yielded the consensus alignment at 3.23 Angstrom, which served as a base for the focused refinements used to make this composite map. Upon reconstruction with imposed C7 symmetry, the two proteasome Beta1-2 subunits of the 20S became merged together. We noticed that the same was happening when the 20S proteasome was reconstructed without an imposed symmetry, suggesting a random distribution of the two subunit types in the Beta rings. Due to the high degree of similarity between the two proteins (>70 percent sequence identity) and the small number of particles, we opted for not continuing with further 3D classification.
50092 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC 5
During a final round of Heterogeneous refinement, input volumes containing a good preliminary homogeneous refinement of the whole complex, APA1 alone, 20S alone and duplicate particles were submitted and forced to undergo hard classification
 emd_54521.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 549.6 549.6 549.6 90.0 90.0 90.0 X Y Z -0.7140532 7.0689178 0.03675891 0.13032712 1.145 1.145 1.145 1.0 AUTHOR Ensemble view of the 20S proteasome from Pyrococcus abyssi and the capping protein Q9UYJ3 (APA1) Other experimental model
Xray structure solved in our lab for APA1
 AF-Q9V122-F1 AlphaFold in silico model
Single chain model used, copies created with local EM fitting tool in ChimeraX
 RIGID BODY FIT
Model building done in coot, refinement in Phenix. No models built for the merged Beta 1-2 chains of the 20S proteasome, due to the identical folding of the two proteins and the very small (single side chains) differences between the two subunits, which prevented effective 3D classification with the small number of particles left. IMPORTANT: the outlier Y204 nonplanar bond was modelled as such based on a higher resolution X-ray model, to be deposited soon.
Cross correlation REAL