EMDB-4002: The human 26S proteasome at 3.9

Basic information

• Entry: Database: EMDB / ID: EMD-4002
• Title: The human 26S proteasome at 3.9

Sample

• Complex: Human 26S proteasome

Function / homology

Function:

positive regulation of inclusion body assembly / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / cytosolic proteasome complex / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / integrator complex / purine ribonucleoside triphosphate binding / meiosis I / proteasome regulatory particle / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / negative regulation of programmed cell death / protein K63-linked deubiquitination / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Cross-presentation of soluble exogenous antigens (endosomes) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / proteasome core complex / Resolution of D-loop Structures through Holliday Junction Intermediates / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / proteasome binding / transcription factor binding / regulation of protein catabolic process / myofibril / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / general transcription initiation factor binding / blastocyst development / polyubiquitin modification-dependent protein binding / immune system process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / protein deubiquitination / endopeptidase activator activity / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / mRNA export from nucleus / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / inclusion body / enzyme regulator activity / ERAD pathway / regulation of proteasomal protein catabolic process / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / stem cell differentiation / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / lipopolysaccharide binding / Degradation of AXIN / Hh mutants are degraded by ERAD / negative regulation of inflammatory response to antigenic stimulus / P-body / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / double-strand break repair via homologous recombination / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / :

Domain/homology:

: / Ubiquitin interaction motif / : / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / 26S proteasome regulatory subunit RPN5 C-terminal domain / PSD13 N-terminal repeats / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / : / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / : / 26S proteasome regulatory subunit RPN11 C-terminal domain / DSS1/SEM1 / Proteasome subunit Rpn10 / 26S Proteasome non-ATPase regulatory subunit 7/8 / DSS1/SEM1 family / DSS1_SEM1 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / : / 26S proteasome regulatory subunit 7, OB domain / : / : / : / PSMD12/CSN4, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Ubiquitin-interacting motif. / PCI/PINT associated module / : / von Willebrand factor type A domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Proteasome subunit alpha 1 / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / HEAT repeats / : / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / von Willebrand factor (vWF) type A domain / VWFA domain profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / von Willebrand factor, type A / AAA ATPase, AAA+ lid domain / AAA+ lid domain / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / MPN domain / MPN domain profile. / Nucleophile aminohydrolases, N-terminal / von Willebrand factor A-like domain superfamily / ATPase family associated with various cellular activities (AAA)

Component:

26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome non-ATPase regulatory subunit 6 / Proteasome subunit beta type-7 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 13

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.9 Å
• Authors: Schweitzer A / Aufderheide A / Rudack T / Beck F
• Citation: Journal: Proc Natl Acad Sci U S A / Year: 2016; Title: Structure of the human 26S proteasome at a resolution of 3.9 Å.; Authors: Andreas Schweitzer / Antje Aufderheide / Till Rudack / Florian Beck / Günter Pfeifer / Jürgen M Plitzko / Eri Sakata / Klaus Schulten / Friedrich Förster / Wolfgang Baumeister / ; Abstract: Protein degradation in eukaryotic cells is performed by the Ubiquitin-Proteasome System (UPS). The 26S proteasome holocomplex consists of a core particle (CP) that proteolytically degrades polyubiquitylated proteins, and a regulatory particle (RP) containing the AAA-ATPase module. This module controls access to the proteolytic chamber inside the CP and is surrounded by non-ATPase subunits (Rpns) that recognize substrates and deubiquitylate them before unfolding and degradation. The architecture of the 26S holocomplex is highly conserved between yeast and humans. The structure of the human 26S holocomplex described here reveals previously unidentified features of the AAA-ATPase heterohexamer. One subunit, Rpt6, has ADP bound, whereas the other five have ATP in their binding pockets. Rpt6 is structurally distinct from the other five Rpt subunits, most notably in its pore loop region. For Rpns, the map reveals two main, previously undetected, features: the C terminus of Rpn3 protrudes into the mouth of the ATPase ring; and Rpn1 and Rpn2, the largest proteasome subunits, are linked by an extended connection. The structural features of the 26S proteasome observed in this study are likely to be important for coordinating the proteasomal subunits during substrate processing.

History

Deposition	May 25, 2016	-
Header (metadata) release	Jun 22, 2016	-
Map release	Jun 22, 2016	-
Update	Jul 26, 2017	-
Current status	Jul 26, 2017	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_4002.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.35 Å

Density

Contour Level	By AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum	-0.19493514 - 0.30707386
Average (Standard dev.)	0.00031536914 (±0.00694399)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 384 384 384 Spacing 384 384 384
Cell	A=B=C: 518.4 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.35	1.35	1.35
M x/y/z	384	384	384
origin x/y/z	0.000	0.000	0.000
length x/y/z	518.400	518.400	518.400
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	384	384	384
D min/max/mean	-0.195	0.307	0.000

Supplemental data

Sample components

Entire : Human 26S proteasome

• Entire: Name: Human 26S proteasome

Components

• Complex: Human 26S proteasome

Supramolecule #1: Human 26S proteasome

• Supramolecule: Name: Human 26S proteasome / type: complex / ID: 1 / Parent: 0
• Source (natural): Organism: Homo sapiens (human)
• Molecular weight: Theoretical: 2.5 MDa

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: cell

Sample preparation

• Concentration: 0.5 mg/mL
• Buffer: pH: 7.5
• Grid: Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
• Vitrification: Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
• Details: This sample was monodisperse.

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 19 / Number real images: 40211 / Average exposure time: 1.5 sec. / Average electron dose: 45.0 e/Ų; Details: Images were collected in movie-mode at 33 frames/s.
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus min: 1.9 µm
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Details: Falcon III
• Particle selection: Number selected: 688742
• CTF correction: Software - Name: CTFFIND (ver. 4.0)

Startup model

Type of model: EMDB MAP
EMDB ID:

2594

• Final reconstruction: Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 461402
• Initial angle assignment: Type: PROJECTION MATCHING
• Final angle assignment: Type: PROJECTION MATCHING