2025-11-05 REL PDBj PDBj PDBj 2023-08-29 2024-09-04 2024-09-04 2025-11-05 Academia Sinica (Taiwan) AS-CDA-109- L08 Taiwan Ministry of Science and Technology (MoST, Taiwan) MOST 109-3114-Y-001-001 Taiwan Ministry of Science and Technology (MoST, Taiwan) MOST 110-2113-M-001- 050-MY3 Taiwan Ministry of Science and Technology (MoST, Taiwan) MOST 110-2311-B-001-013-MY3 Taiwan Local refinement cryo-EM map of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub, focused on Rpn3/Rpn7 region. Hsu STD Draczkowski P Wang YS protein degradation, macromolecular complex, ubiquitin-proteasome system, CYTOSOLIC PROTEIN Draczkowski P Chen SN Chen T Wang YS Shih HA Huang JYC Tsai MC Lin SY Lin S Viner R Chang YC Wu KP Hsu SD Structural basis of K11/K48-branched ubiquitin chain recognition by the human 26S proteasome. Nat Commun UK 16 9094 9094 2025 41093839 doi:10.1038/s41467-025-64719-x 2041-1723 EMD-36645 other EM volume
composite map
 PDB 8JTI unspecified
model corresponding to the composite map
 EMDB EMD-37327 associated EM volume EMDB EMD-36645 other EM volume
composite map
 Human 26S proteasome Human 26S proteasome 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26
Images of double-capped (RP-CP-RP) 26S proteasome particles were split in half. After combining with subset of single-capped (RP-CP) complexes the signal in particle images was partially subtracted leaving only the signal of 19S RP together with alpha subunits of the 20S CP proteasomal subcomplex.
2.5 19S regulatory particle (RP) of human 26S proteasome 1 1 2 3 4 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Homo sapiens AAA+-ATPase of 19S regulatory particle (RP) of human 26S proteasome 2 1 2 3 4 19 20 Homo sapiens alpha subunits of the 20S core particle (CP) of human 26S proteasome 1 5 6 7 8 9 10 11 Homo sapiens K11/K48-branched ubiquitin (Ub) chain composed of four Ub. 1 26 Homo sapiens 8 singleParticle particle 1 7.6 20.0 C8H18N2O4S HEPES 40.0 NaCl sodium chloride 5.0 MgCl2 magnesium chloride 2.0 C2H6OS 2-Mercaptoethanol 0.5 C12H8N2 1,10-Phenanthroline 2.0 C10H16N5O13P3 adenosine triphosphate Quantifoil R1.2/1.3 COPPER 300 GLOW DISCHARGE AIR
20 mA
 ETHANE 100 277.15 FEI VITROBOT MARK IV
incubation time= 3 s blotting time= 2.5 s.
The complex was additionally supplemented with an excess of preformed and SEC-purified RPN13:UCHL5 complex.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.2 1.8 70000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 20 GATAN K3 (6k x 4k) 3 15242 1.8 49.0 1 2695911 CTFFIND 4.1 PHASE FLIPPING AND AMPLITUDE CORRECTION Generated by cryoSPARC using Ab-initio Reconstruction job type. 1 C1 FOURIER SPACE 3.9 FSC 0.143 CUT-OFF cryoSPARC 3.1 Local focused refinement 52216 MAXIMUM LIKELIHOOD RELION 3.1
Performed in Relion.
 MAXIMUM LIKELIHOOD cryoSPARC 3.1 Non-uniform Refinment
Performed in cryoSPARC using Local focused refinement job type.
 6 cryoSPARC 3.1
3D variability analysis (3DVA) followed by Heterogenous refinement using 3DVA cluster volumes as starting references.
 emd_37327.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 560.0 560.0 560.0 90.0 90.0 90.0 X Y Z -0.46880832 1.5397367 -0.002348461 0.043926585 1.4 1.4 1.4 0.5 AUTHOR Local refinement cryo-EM map of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub, focused on Rpn3/Rpn7 region. emd_37327_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 560.0 560.0 560.0 90.0 90.0 90.0 X Y Z -1.0526869 1.9216081 0.00133429 0.13503271 1.4 1.4 1.4 AUTHOR Local refinement cryo-EM half map of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub, focused on Rpn3/Rpn7 region. emd_37327_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 560.0 560.0 560.0 90.0 90.0 90.0 X Y Z -0.9860091 1.9460517 0.001286256 0.1350071 1.4 1.4 1.4 AUTHOR Local refinement cryo-EM half map of human 26S RP (Eb state) bound to K11/K48-branched ubiquitin (Ub) chain composed of four Ub, focused on Rpn3/Rpn7 region.