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- PDB-3j9i: Thermoplasma acidophilum 20S proteasome -

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Basic information

Entry
Database: PDB / ID: 3j9i
TitleThermoplasma acidophilum 20S proteasome
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE / proteasome
Function / homology
Function and homology information


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 / endopeptidase activity / cytoplasm
Similarity search - Function
Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 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 ...Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 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 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome subunit alpha / Proteasome subunit beta
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi, X. / Mooney, P. / Zheng, S. / Booth, C. / Braunfeld, M.B. / Gubbens, S. / Agard, D.A. / Cheng, Y.
Citation
Journal: Nat Methods / Year: 2013
Title: Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.
Authors: Xueming Li / Paul Mooney / Shawn Zheng / Christopher R Booth / Michael B Braunfeld / Sander Gubbens / David A Agard / Yifan Cheng /
Abstract: In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of ...In recent work with large high-symmetry viruses, single-particle electron cryomicroscopy (cryo-EM) has achieved the determination of near-atomic-resolution structures by allowing direct fitting of atomic models into experimental density maps. However, achieving this goal with smaller particles of lower symmetry remains challenging. Using a newly developed single electron-counting detector, we confirmed that electron beam-induced motion substantially degrades resolution, and we showed that the combination of rapid readout and nearly noiseless electron counting allow image blurring to be corrected to subpixel accuracy, restoring intrinsic image information to high resolution (Thon rings visible to ∼3 Å). Using this approach, we determined a 3.3-Å-resolution structure of an ∼700-kDa protein with D7 symmetry, the Thermoplasma acidophilum 20S proteasome, showing clear side-chain density. Our method greatly enhances image quality and data acquisition efficiency-key bottlenecks in applying near-atomic-resolution cryo-EM to a broad range of protein samples.
#1: Journal: To be Published
Title: Side-chain-directed model and map validation for 3D electron cryomicroscopy
Authors: Barad, B.A. / Echols, N. / Wang, R.Y.-R. / Cheng, Y. / DiMaio, F. / Adams, P.D. / Fraser, J.S.
History
DepositionFeb 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5623
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-5623
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: Proteasome subunit alpha
Z: Proteasome subunit beta
F: Proteasome subunit alpha
M: Proteasome subunit beta
T: Proteasome subunit alpha
1: Proteasome subunit beta
G: Proteasome subunit alpha
N: Proteasome subunit beta
U: Proteasome subunit alpha
2: Proteasome subunit beta
A: Proteasome subunit alpha
H: Proteasome subunit beta
O: Proteasome subunit alpha
V: Proteasome subunit beta
B: Proteasome subunit alpha
I: Proteasome subunit beta
P: Proteasome subunit alpha
W: Proteasome subunit beta
C: Proteasome subunit alpha
J: Proteasome subunit beta
Q: Proteasome subunit alpha
X: Proteasome subunit beta
D: Proteasome subunit alpha
K: Proteasome subunit beta
R: Proteasome subunit alpha
Y: Proteasome subunit beta
E: Proteasome subunit alpha
L: Proteasome subunit beta


Theoretical massNumber of molelcules
Total (without water)658,99628
Polymers658,99628
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 24776.281 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmA, Ta1288 / Production host: Escherichia coli (E. coli)
References: UniProt: P25156, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PsmB


Mass: 22294.848 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmB, Ta0612 / Production host: Escherichia coli (E. coli)
References: UniProt: P28061, proteasome endopeptidase complex

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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
IDNameTypeParent-ID
1Thermoplasma acidophilum 20S proteasomeRIBOSOME0
2proteasome alpha subunit1
3proteasome beta subunit1
Molecular weightValue: 0.7 MDa / Experimental value: YES
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil grid
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temp: 120 K / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK III)

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Jun 1, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 31000 X / Nominal defocus max: 1900 nm / Nominal defocus min: 800 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 600
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1MDFFmodel fitting
2UCSF Chimeramodel fitting
3FREALIGN3D reconstructionGPU-enhanced FREALIGN
CTF correctionDetails: Each Particle
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionMethod: FREALIGN / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126729 / Nominal pixel size: 1.2156 Å / Actual pixel size: 1.2156 Å / Details: Gold Standard FSC, imposed symmetry: D7 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: REFINEMENT PROTOCOL--Flexible
Atomic model buildingPDB-ID: 1PMA

1pma


Accession code: 1PMA / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms46228 0 0 0 46228

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