2026-08-12 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY 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 Focused map of the 20S proteasome from Pyrococcus abyssi in complex with Q9UYJ3 (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 Focused map of the 20S proteasome from Pyrococcus abyssi in complex with Q9UYJ3 (APA1) To Be Published 0353 EMDB EMD-54518 associated EM volume 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 singleParticle particle 8.0 ETHANE-PROPANE 100 298 FEI VITROBOT MARK IV TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 2.7 1.0 2.5 NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 40.0 1 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 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_54518.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 -0.5848336 1.1900442 0.00019446237 0.025616085 1.145 1.145 1.145 0.26 AUTHOR Unprocessed focused map of the 20S proteasome from Pyrococcus abyssi in complex with 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.
Cross correlation REAL emd_54518_additional_1.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 -2.61684 4.2413507 0.00019446235 0.08354462 1.145 1.145 1.145 AUTHOR sharpened map used for model building emd_54518_half_map_1.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 -0.7252702 1.3265043 0.0004643995 0.07539468 1.145 1.145 1.145 AUTHOR emd_54518_half_map_2.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 -0.62300634 1.379945 0.0004622237 0.075670294 1.145 1.145 1.145 AUTHOR