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- PDB-6he8: PAN-proteasome in state 1 -

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Basic information

Entry
Database: PDB / ID: 6he8
TitlePAN-proteasome in state 1
Components
  • (Proteasome subunit ...) x 2
  • Proteasome-activating nucleotidase
KeywordsHYDROLASE / PAN / Proteasome / AAA-ATPase / Archaea / hydrolase
Function / homologyAAA+ lid domain / Proteasome subunit / Proteasome B-type subunit / Proteasome-activating nucleotidase PAN / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / Proteasomal ATPase OB C-terminal domain / ATPase family associated with various cellular activities (AAA) / Proteasome subunit A N-terminal signature / Proteasome alpha subunit, archaeal ...AAA+ lid domain / Proteasome subunit / Proteasome B-type subunit / Proteasome-activating nucleotidase PAN / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / Proteasomal ATPase OB C-terminal domain / ATPase family associated with various cellular activities (AAA) / Proteasome subunit A N-terminal signature / Proteasome alpha subunit, archaeal / Proteasomal ATPase OB C-terminal domain / Proteasome alpha-type subunits signature. / AAA-protein family signature. / Proteasome beta-type subunits signature. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome beta-type subunit, conserved site / 26S proteasome regulatory subunit P45-like / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / AAA+ ATPase domain / Proteasome, subunit alpha/beta / Proteasome alpha-subunit, N-terminal domain / Peptidase T1A, proteasome beta-subunit / proteasome-activating nucleotidase complex / protein unfolding / proteasome core complex, beta-subunit complex / proteasome endopeptidase complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / ATPase activity / ATP binding / cytoplasm / Proteasome-activating nucleotidase / Proteasome subunit alpha / Proteasome subunit beta
Function and homology information
Specimen sourceArchaeoglobus fulgidus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6.86 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 20, 2018 / Release: Dec 26, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 26, 2018Structure modelrepositoryInitial release
1.1Jan 16, 2019Structure modelData collection / Database referencescitation_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
Polyers954,65634
Non-polymers2,57710
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)164550
ΔGint (kcal/M)-566
Surface area (Å2)294750
MethodPISA

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Components

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

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


Mass: 27156.160 Da / Num. of mol.: 14 / Mutation: 0
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: psmA, AF_0490Glutamate carboxypeptidase II / Production host: Escherichia coli (E. coli)
References: UniProt: O29760, proteasome endopeptidase complex
#2: Protein/peptide
Proteasome subunit beta / / 20S proteasome beta subunit / Proteasome core protein PsmB


Mass: 22132.283 Da / Num. of mol.: 14 / Mutation: 0
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: psmB, AF_0481 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9P996, proteasome endopeptidase complex

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Protein/peptide , 1 types, 6 molecules HIKLMJ

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


Mass: 44102.977 Da / Num. of mol.: 6 / Mutation: 0
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
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


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg / Magnesium
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1PAN-proteasomeCOMPLEX1, 2, 30RECOMBINANT
220S-proteasomeCOMPLEX1, 21RECOMBINANT
3Proteasome-activating nucleotidase (PAN)COMPLEX31RECOMBINANT
Molecular weightValue: 1.25 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
21224325Archaeoglobus fulgidus DSM 4304 (archaea)
32224325Archaeoglobus fulgidus DSM 4304 (archaea)
43224325Archaeoglobus fulgidus DSM 4304 (archaea)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
21562Escherichia coli (E. coli)
32562Escherichia coli (E. coli)
43562Escherichia coli (E. coli)
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
MicroscopyMicroscope model: 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
3D reconstructionResolution: 6.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 38230 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

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