+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-0211 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 20S proteasome from Archaeoglobus fulgidus | |||||||||
![]() | 20S control | |||||||||
![]() |
| |||||||||
![]() | PAN / Proteasome / AAA-ATPase / Archaea / hydrolase | |||||||||
Function / homology | ![]() proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / ubiquitin-dependent protein catabolic process / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.69 Å | |||||||||
![]() | Majumder P / Rudack T | |||||||||
![]() | ![]() Title: Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle. Authors: Parijat Majumder / Till Rudack / Florian Beck / Radostin Danev / Günter Pfeifer / István Nagy / Wolfgang Baumeister / ![]() Abstract: Proteasomes occur in all three domains of life, and are the principal molecular machines for the regulated degradation of intracellular proteins. They play key roles in the maintenance of protein ...Proteasomes occur in all three domains of life, and are the principal molecular machines for the regulated degradation of intracellular proteins. They play key roles in the maintenance of protein homeostasis, and control vital cellular processes. While the eukaryotic 26S proteasome is extensively characterized, its putative evolutionary precursor, the archaeal proteasome, remains poorly understood. The primordial archaeal proteasome consists of a 20S proteolytic core particle (CP), and an AAA-ATPase module. This minimal complex degrades protein unassisted by non-ATPase subunits that are present in a 26S proteasome regulatory particle (RP). Using cryo-EM single-particle analysis, we determined structures of the archaeal CP in complex with the AAA-ATPase PAN (proteasome-activating nucleotidase). Five conformational states were identified, elucidating the functional cycle of PAN, and its interaction with the CP. Coexisting nucleotide states, and correlated intersubunit signaling features, coordinate rotation of the PAN-ATPase staircase, and allosterically regulate N-domain motions and CP gate opening. These findings reveal the structural basis for a sequential around-the-ring ATPase cycle, which is likely conserved in AAA-ATPases. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 2.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 10.9 KB 10.9 KB | Display Display | ![]() |
Images | ![]() | 177.2 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 221.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 221 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6he7MC ![]() 0209C ![]() 0210C ![]() 0212C ![]() 0213C ![]() 0214C ![]() 0215C ![]() 0216C ![]() 6he4C ![]() 6he5C ![]() 6he8C ![]() 6he9C ![]() 6heaC ![]() 6hecC ![]() 6hedC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 20S control | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : 20S proteasome
Entire | Name: 20S proteasome |
---|---|
Components |
|
-Supramolecule #1: 20S proteasome
Supramolecule | Name: 20S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 710 KDa |
-Macromolecule #1: Proteasome subunit alpha
Macromolecule | Name: Proteasome subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 26.333248 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: ITVFSPDGRL FQVEYAREAV KRGATAIGIK CKEGVILIAD KRVGSKLLEA DTIEKIYKID EHICAATSGL VADARVLIDR ARIEAQINR LTYDEPITVK ELAKKICDFK QQYTQYGGVR PFGVSLLIAG VDEVPKLYET DPSGALLEYK ATAIGMGRNA V TEFFEKEY ...String: ITVFSPDGRL FQVEYAREAV KRGATAIGIK CKEGVILIAD KRVGSKLLEA DTIEKIYKID EHICAATSGL VADARVLIDR ARIEAQINR LTYDEPITVK ELAKKICDFK QQYTQYGGVR PFGVSLLIAG VDEVPKLYET DPSGALLEYK ATAIGMGRNA V TEFFEKEY RDDLSFDDAM VLGLVAMGLS IESELVPENI EVGYVKVDDR TFKEVSPEEL KPYVERANER IRELLKK UniProtKB: Proteasome subunit alpha |
-Macromolecule #2: Proteasome subunit beta
Macromolecule | Name: Proteasome subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 22.132283 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: TTTVGLVCKD GVVMATEKRA TMGNFIASKA AKKIYQIADR MAMTTAGSVG DAQFLARIIK IEANLYEIRR ERKPTVRAIA TLTSNLLNS YRYFPYLVQL LIGGIDSEGK SIYSIDPIGG AIEEKDIVAT GSGSLTAYGV LEDRFTPEIG VDEAVELAVR A IYSAMKRD ...String: TTTVGLVCKD GVVMATEKRA TMGNFIASKA AKKIYQIADR MAMTTAGSVG DAQFLARIIK IEANLYEIRR ERKPTVRAIA TLTSNLLNS YRYFPYLVQL LIGGIDSEGK SIYSIDPIGG AIEEKDIVAT GSGSLTAYGV LEDRFTPEIG VDEAVELAVR A IYSAMKRD SASGDGIDVV KITEDEFYQY SPEEVEQILA KFRK UniProtKB: Proteasome subunit beta |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.1 |
---|---|
Vitrification | Cryogen name: ETHANE-PROPANE |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: PDB ENTRY |
---|---|
Final reconstruction | Applied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 105384 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
---|---|
Output model | ![]() PDB-6he7: |