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- PDB-6hed: PAN-proteasome in state 5 -

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Basic information

Entry
Database: PDB / ID: 6hed
TitlePAN-proteasome in state 5
Components
  • (Proteasome subunit ...) x 2
  • Proteasome-activating nucleotidase
KeywordsHYDROLASE / PAN / Proteasome / AAA-ATPase / Archaea
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / protein unfolding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Proteasome-activating nucleotidase PAN / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / 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-activating nucleotidase PAN / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / 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 / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Proteasome-activating nucleotidase / Proteasome subunit alpha / Proteasome subunit beta
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.95 Å
AuthorsMajumder, P. / Rudack, T. / Beck, F. / Baumeister, W.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
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
DepositionAug 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

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Assembly

Deposited unit
A: Proteasome subunit alpha
a: Proteasome subunit alpha
B: Proteasome subunit alpha
b: Proteasome subunit alpha
C: Proteasome subunit alpha
c: Proteasome subunit alpha
D: Proteasome subunit alpha
d: Proteasome subunit alpha
E: Proteasome subunit alpha
e: Proteasome subunit alpha
F: Proteasome subunit alpha
f: Proteasome subunit alpha
G: Proteasome subunit alpha
g: Proteasome subunit alpha
1: Proteasome subunit beta
h: Proteasome subunit beta
2: Proteasome subunit beta
i: Proteasome subunit beta
3: Proteasome subunit beta
j: Proteasome subunit beta
4: Proteasome subunit beta
k: Proteasome subunit beta
5: Proteasome subunit beta
l: Proteasome subunit beta
6: Proteasome subunit beta
m: Proteasome subunit beta
7: Proteasome subunit beta
n: Proteasome subunit beta
H: Proteasome-activating nucleotidase
I: Proteasome-activating nucleotidase
K: Proteasome-activating nucleotidase
L: Proteasome-activating nucleotidase
M: Proteasome-activating nucleotidase
J: Proteasome-activating nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)957,23444
Polymers954,65634
Non-polymers2,57710
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area164240 Å2
ΔGint-565 kcal/mol
Surface area295530 Å2
MethodPISA

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Components

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Proteasome subunit ... , 2 types, 28 molecules AaBbCcDdEeFfGg1h2i3j4k5l6m7n

#1: Protein
Proteasome subunit alpha / / 20S proteasome alpha subunit / Proteasome core protein PsmA


Mass: 27156.160 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Gene: psmA, AF_0490 / Production host: Escherichia coli (E. coli)
References: UniProt: O29760, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / / 20S proteasome beta subunit / Proteasome core protein PsmB


Mass: 22132.283 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Gene: psmB, AF_0481 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P996, proteasome endopeptidase complex

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Protein , 1 types, 6 molecules HIKLMJ

#3: Protein
Proteasome-activating nucleotidase / PAN / Proteasomal ATPase / Proteasome regulatory ATPase / Proteasome regulatory particle


Mass: 44102.977 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Gene: pan, AF_1976 / Production host: Escherichia coli (E. coli) / References: UniProt: O28303

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Non-polymers , 3 types, 10 molecules

#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1PAN-proteasomeCOMPLEX#1-#30RECOMBINANT
220S-proteasomeCOMPLEX#1-#21RECOMBINANT
3Proteasome-activating nucleotidase (PAN)COMPLEX#31RECOMBINANT
Molecular weightValue: 1.25 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Archaeoglobus fulgidus DSM 4304 (archaea)224325
32Archaeoglobus fulgidus DSM 4304 (archaea)224325
43Archaeoglobus fulgidus DSM 4304 (archaea)224325
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Buffer solutionpH: 7.1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
4MotionCorr2CTF correction
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30758 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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