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- PDB-8oix: CryoEM structure of 20S Trichomonas vaginalis proteasome in compl... -

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Basic information

Entry
Database: PDB / ID: 8oix
TitleCryoEM structure of 20S Trichomonas vaginalis proteasome in complex with proteasome inhibitor Salinosporamid A
Components
  • (Family T1, proteasome alpha subunit, threonine ...) x 4
  • (Proteasome subunit ...) x 8
  • Family T1, proteasome beta subunit, threonine peptidase
  • proteasome endopeptidase complex
KeywordsHYDROLASE / Proteasome / 20S / Trichomonas vaginalis / covalently bound Salinosporamide A / Marizomib
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 / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / 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 subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / 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
Similarity search - Domain/homology
Chem-SA1 / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta / Proteasome subunit alpha type / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta / proteasome endopeptidase complex / Proteasome subunit beta / Family T1, proteasome beta subunit, threonine peptidase / Family T1, proteasome alpha subunit, threonine peptidase ...Chem-SA1 / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta / Proteasome subunit alpha type / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta / proteasome endopeptidase complex / Proteasome subunit beta / Family T1, proteasome beta subunit, threonine peptidase / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit beta / Proteasome subunit beta / Proteasome subunit alpha type / Family T1, proteasome alpha subunit, threonine peptidase / Proteasome subunit alpha type
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsSilhan, J. / Fajtova, P. / Boura, E.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission846688European Union
CitationJournal: To Be Published
Title: Tv20S proteasome in the complex with marizomib
Authors: Silhan, J. / Fajtova, P. / O'Donoghue, A. / Boura, E.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 2.0Apr 17, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Family T1, proteasome alpha subunit, threonine peptidase
B: Family T1, proteasome alpha subunit, threonine peptidase
C: Proteasome subunit alpha type
D: Proteasome subunit alpha type
E: Proteasome subunit alpha type
F: Family T1, proteasome alpha subunit, threonine peptidase
G: Family T1, proteasome alpha subunit, threonine peptidase
H: Proteasome subunit beta
I: proteasome endopeptidase complex
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Family T1, proteasome beta subunit, threonine peptidase
O: Family T1, proteasome alpha subunit, threonine peptidase
P: Family T1, proteasome alpha subunit, threonine peptidase
Q: Proteasome subunit alpha type
R: Proteasome subunit alpha type
S: Proteasome subunit alpha type
T: Family T1, proteasome alpha subunit, threonine peptidase
U: Family T1, proteasome alpha subunit, threonine peptidase
V: Proteasome subunit beta
W: proteasome endopeptidase complex
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit beta
a: Proteasome subunit beta
b: Family T1, proteasome beta subunit, threonine peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)708,40632
Polymers707,28828
Non-polymers1,1174
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Negative Stain with Uranyl Acetate SEC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area117030 Å2
ΔGint-412 kcal/mol
Surface area177780 Å2
MethodPISA

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Components

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Family T1, proteasome alpha subunit, threonine ... , 4 types, 8 molecules AOBPFTGU

#1: Protein Family T1, proteasome alpha subunit, threonine peptidase


Mass: 26511.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_267300 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2F568
#2: Protein Family T1, proteasome alpha subunit, threonine peptidase


Mass: 25444.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_103780 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2FJV7
#6: Protein Family T1, proteasome alpha subunit, threonine peptidase


Mass: 25682.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_206040 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2E1I9
#7: Protein Family T1, proteasome alpha subunit, threonine peptidase


Mass: 27067.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_185200 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2D8G5

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Proteasome subunit ... , 8 types, 16 molecules CQDRESHVJXKYLZMa

#3: Protein Proteasome subunit alpha type /


Mass: 27989.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_058050 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2FT79
#4: Protein Proteasome subunit alpha type /


Mass: 26306.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_340740 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2DTN3
#5: Protein Proteasome subunit alpha type /


Mass: 27330.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_293540 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2FCM7
#8: Protein Proteasome subunit beta /


Mass: 21930.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_127250 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2E7Z2
#10: Protein Proteasome subunit beta /


Mass: 23028.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_286960 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2F3H9
#11: Protein Proteasome subunit beta /


Mass: 21421.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_403280 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2F8W4
#12: Protein Proteasome subunit beta /


Mass: 22572.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_013010 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2DD57
#13: Protein Proteasome subunit beta /


Mass: 25001.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_152400 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2F716

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Protein , 2 types, 4 molecules IWNb

#9: Protein proteasome endopeptidase complex /


Mass: 26869.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_231360 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A2F2T6, proteasome endopeptidase complex
#14: Protein Family T1, proteasome beta subunit, threonine peptidase


Mass: 26486.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_290960 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A2F3X4

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Non-polymers , 1 types, 4 molecules

#15: Chemical
ChemComp-SA1 / (3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE / Salinosporamide A, bound form


Mass: 279.332 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H21NO4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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

ComponentName: Ternary complex of 20S proteasome from Trichomonas vaginalis
Type: COMPLEX
Details: Subunits beta 1 and beta 2 a covalently attached to protease inhibitor marizomib (Salinosporamid A)
Entity ID: #1-#14 / Source: RECOMBINANT
Molecular weightValue: 0.704 MDa / Experimental value: NO
Source (natural)Organism: Trichomonas vaginalis G3 (eukaryote)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESHEPES1
2150 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3600 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7983
EM imaging opticsEnergyfilter name: TFS Selectris
Image scansWidth: 4096 / Height: 4096

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 2303719
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14257 / Details: Standard Homo Refine job in Cryosparc v4 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00448680
ELECTRON MICROSCOPYf_angle_d0.60865880
ELECTRON MICROSCOPYf_dihedral_angle_d13.03717850
ELECTRON MICROSCOPYf_chiral_restr0.0457434
ELECTRON MICROSCOPYf_plane_restr0.0088518

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