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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0215 | |||||||||
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Title | PAN-proteasome in state 4 | |||||||||
![]() | PSC of PAN-proteasome in state 4 | |||||||||
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![]() | PAN / Proteasome / AAA-ATPase / Archaea / hydrolase | |||||||||
Function / homology | ![]() proteasome-activating nucleotidase complex / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasome endopeptidase complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process ...proteasome-activating nucleotidase complex / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasome endopeptidase complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.95 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.9 KB 16.9 KB | Display Display | ![]() |
Images | ![]() | 76.1 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() | 1.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hecMC ![]() 0209C ![]() 0210C ![]() 0211C ![]() 0212C ![]() 0213C ![]() 0214C ![]() 0216C ![]() 6he4C ![]() 6he5C ![]() 6he7C ![]() 6he8C ![]() 6he9C ![]() 6heaC ![]() 6hedC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | PSC of PAN-proteasome in state 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: AAAob of PAN-proteasome in state 4
File | emd_0215_additional.map | ||||||||||||
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Annotation | AAAob of PAN-proteasome in state 4 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : PAN-proteasome
Entire | Name: PAN-proteasome |
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Components |
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-Supramolecule #1: PAN-proteasome
Supramolecule | Name: PAN-proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 1.25 MDa |
-Supramolecule #2: 20S-proteasome
Supramolecule | Name: 20S-proteasome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Proteasome-activating nucleotidase (PAN)
Supramolecule | Name: Proteasome-activating nucleotidase (PAN) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Proteasome subunit alpha
Macromolecule | Name: Proteasome subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 27.15616 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QMGYDRAITV FSPDGRLFQV EYAREAVKRG ATAIGIKCKE GVILIADKRV GSKLLEADTI EKIYKIDEHI CAATSGLVAD ARVLIDRAR IEAQINRLTY DEPITVKELA KKICDFKQQY TQYGGVRPFG VSLLIAGVDE VPKLYETDPS GALLEYKATA I GMGRNAVT ...String: QMGYDRAITV FSPDGRLFQV EYAREAVKRG ATAIGIKCKE GVILIADKRV GSKLLEADTI EKIYKIDEHI CAATSGLVAD ARVLIDRAR IEAQINRLTY DEPITVKELA KKICDFKQQY TQYGGVRPFG VSLLIAGVDE VPKLYETDPS GALLEYKATA I GMGRNAVT EFFEKEYRDD LSFDDAMVLG LVAMGLSIES ELVPENIEVG YVKVDDRTFK EVSPEELKPY VERANERIRE LL KK UniProtKB: Proteasome subunit alpha |
-Macromolecule #2: Proteasome subunit beta
Macromolecule | Name: Proteasome subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex |
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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 |
-Macromolecule #3: Proteasome-activating nucleotidase
Macromolecule | Name: Proteasome-activating nucleotidase / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 44.102977 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: LLEKLKKLEE DYYKLRELYR RLEDEKKFIE SERIRYEREV RRLRSEVERL RSPPLLVGVV SDILEDGRVV VKSSTGPKFV VNTSQYINE EELKPGARVA LNQQTLAIVN VLPTSKDPMV YGFEVEEKPE VSYEDIGGLD VQIEEIREAV ELPLLKPELF A EVGIEPPK ...String: LLEKLKKLEE DYYKLRELYR RLEDEKKFIE SERIRYEREV RRLRSEVERL RSPPLLVGVV SDILEDGRVV VKSSTGPKFV VNTSQYINE EELKPGARVA LNQQTLAIVN VLPTSKDPMV YGFEVEEKPE VSYEDIGGLD VQIEEIREAV ELPLLKPELF A EVGIEPPK GVLLYGPPGT GKTLLAKAVA NQTRATFIRV VGSEFVQKYI GEGARLVREV FQLAKEKAPS IIFIDELDAI AA RRTNSDT SGDREVQRTM MQLLAELDGF DPRGDVKVIG ATNRIDILDP AILRPGRFDR IIEVPLPTFE GRIQIFKIHT RKM KLAEDV DFKELARITE GASGADIKAI CTEAGMFAIR EERAKVTMLD FTKAIEKVLK KTTPIPDLKG VMFV UniProtKB: Proteasome-activating nucleotidase |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.1 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 36385 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-6hec: |