8OIX

CryoEM structure of 20S Trichomonas vaginalis proteasome in complex with proteasome inhibitor Salinosporamid A

PDB DOI: https://doi.org/10.2210/pdb8OIX/pdb
EM Map EMD-16901: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Trichomonas vaginalis G3
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-03-23 Released: 2024-04-10
Deposition Author(s): Silhan, J., Fajtova, P., Boura, E.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Tv20S proteasome in the complex with marizomib

Silhan, J., Fajtova, P., O'Donoghue, A., Boura, E.

To be published.

Macromolecule Content

Total Structure Weight: 708.41 kDa
Atom Count: 47,786
Modelled Residue Count: 6,150
Deposited Residue Count: 6,398
Unique protein chains: 14

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Family T1, proteasome alpha subunit, threonine peptidase	A, O	241	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_267300
UniProt
Find proteins for A2F568 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2F568 Go to UniProtKB: A2F568
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2F568
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Family T1, proteasome alpha subunit, threonine peptidase	B, P	232	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_103780
UniProt
Find proteins for A2FJV7 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2FJV7 Go to UniProtKB: A2FJV7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2FJV7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type	C, Q	251	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_058050
UniProt
Find proteins for A2FT79 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2FT79 Go to UniProtKB: A2FT79
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2FT79
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type	D, R	235	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_340740
UniProt
Find proteins for A2DTN3 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2DTN3 Go to UniProtKB: A2DTN3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2DTN3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type	E, S	251	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_293540
UniProt
Find proteins for A2FCM7 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2FCM7 Go to UniProtKB: A2FCM7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2FCM7
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Family T1, proteasome alpha subunit, threonine peptidase	F, T	233	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_206040
UniProt
Find proteins for A2E1I9 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2E1I9 Go to UniProtKB: A2E1I9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2E1I9
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Family T1, proteasome alpha subunit, threonine peptidase	G, U	240	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_185200
UniProt
Find proteins for A2D8G5 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2D8G5 Go to UniProtKB: A2D8G5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2D8G5
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta	H, V	204	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_127250
UniProt
Find proteins for A2E7Z2 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2E7Z2 Go to UniProtKB: A2E7Z2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2E7Z2
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
proteasome endopeptidase complex	I, W	244	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_231360 EC: 3.4.25.1
UniProt
Find proteins for A2F2T6 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2F2T6 Go to UniProtKB: A2F2T6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2F2T6
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta	J, X	206	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_286960
UniProt
Find proteins for A2F3H9 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2F3H9 Go to UniProtKB: A2F3H9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2F3H9
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta	K, Y	191	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_403280
UniProt
Find proteins for A2F8W4 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2F8W4 Go to UniProtKB: A2F8W4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2F8W4
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta	L, Z	203	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_013010
UniProt
Find proteins for A2DD57 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2DD57 Go to UniProtKB: A2DD57
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2DD57
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta	AA [auth a], M	224	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_152400
UniProt
Find proteins for A2F716 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2F716 Go to UniProtKB: A2F716
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2F716
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Family T1, proteasome beta subunit, threonine peptidase	BA [auth b], N	244	Trichomonas vaginalis G3	Mutation(s): 0 Gene Names: TVAG_290960
UniProt
Find proteins for A2F3X4 (Trichomonas vaginalis (strain ATCC PRA-98 / G3)) Explore A2F3X4 Go to UniProtKB: A2F3X4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2F3X4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SA1 (Subject of Investigation/LOI) Query on SA1 Download Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain DA [auth I] SDF format, chain EA [auth V] SDF format, chain FA [auth W] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth I] MOL2 format, chain EA [auth V] MOL2 format, chain FA [auth W]	CA [auth H], DA [auth I], EA [auth V], FA [auth W]	(3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE C₁₅ H₂₁ N O₄ YVABESCRHMBHJD-FUQNVFFISA-N		Interactions Focus chain CA [auth H] Focus chain DA [auth I] Focus chain EA [auth V] Focus chain FA [auth W] Interactions & Density Focus chain CA [auth H] Focus chain DA [auth I] Focus chain EA [auth V] Focus chain FA [auth W]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-04-10

Deposition Author(s):

Silhan, J.

Fajtova, P.

Boura, E.

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	846688

Revision History (Full details and data files)

Version 1.0: 2024-04-10
Type: Initial release
Version 2.0: 2024-04-17
Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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8OIX

CryoEM structure of 20S Trichomonas vaginalis proteasome in complex with proteasome inhibitor Salinosporamid A

Tv20S proteasome in the complex with marizomib

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)