5BXN | pdb_00005bxn

Yeast 20S proteasome beta2-G170A mutant in complex with Bortezomib

PDB DOI: https://doi.org/10.2210/pdb5BXN/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Saccharomyces cerevisiae S288C
Mutation(s): Yes

Deposited: 2015-06-09 Released: 2016-06-15
Deposition Author(s): Huber, E.M., Groll, M.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.218 (Depositor), 0.223 (DCC)
R-Value Work:
0.198 (Depositor), 0.203 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

Literature

Defective immuno- and thymoproteasome assembly causes severe immunodeficiency.

Treise, I., Huber, E.M., Klein-Rodewald, T., Heinemeyer, W., Grassmann, S.A., Basler, M., Adler, T., Rathkolb, B., Helming, L., Andres, C., Klaften, M., Landbrecht, C., Wieland, T., Strom, T.M., McCoy, K.D., Macpherson, A.J., Wolf, E., Groettrup, M., Ollert, M., Neff, F., Gailus-Durner, V., Fuchs, H., Hrabe de Angelis, M., Groll, M., Busch, D.H.

(2018) Sci Rep 8: 5975-5975

PubMed: 29654304 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-018-24199-0
Primary Citation Related Structures:
5BXL, 5BXN

PubMed Abstract:
By N-ethyl-N-nitrosourea (ENU) mutagenesis, we generated the mutant mouse line TUB6 that is characterised by severe combined immunodeficiency (SCID) and systemic sterile autoinflammation in homozygotes, and a selective T cell defect in heterozygotes. The causative missense point mutation results in the single amino acid exchange G170W in multicatalytic endopeptidase complex subunit-1 (MECL-1), the β2i-subunit of the immuno- and thymoproteasome. Yeast mutagenesis and crystallographic data suggest that the severe TUB6-phenotype compared to the MECL-1 knockout mouse is caused by structural changes in the C-terminal appendage of β2i that prevent the biogenesis of immuno- and thymoproteasomes. Proteasomes are essential for cell survival, and defective proteasome assembly causes selective death of cells expressing the mutant MECL-1, leading to the severe immunological phenotype. In contrast to the immunosubunits β1i (LMP2) and β5i (LMP7), mutations in the gene encoding MECL-1 have not yet been assigned to human disorders. The TUB6 mutant mouse line exemplifies the involvement of MECL-1 in immunopathogenesis and provides the first mouse model for primary immuno- and thymoproteasome-associated immunodeficiency that may also be relevant in humans.

Organizational Affiliation

Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstr. 30, 81675, Munich, Germany.

German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.

German Center for Infection Research (DZIF), Trogerstr. 30, 81675, Munich, Germany.

Center for Integrated Protein Science at the Department Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany.

Institute of Pathology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.

Division of Immunology, Department of Biology, University of Konstanz, Universitaetsstr. 10, 78457, Konstanz, Germany.

Institute for Molecular Animal Breeding and Biotechnology, Gene Center of the Ludwig-Maximilians-Universität München, Feodor-Lynen Str. 25, 81377, Munich, Germany.

German Center for Diabetes Research (DZD), Ingostädter Landstr. 1, 85764, Neuherberg, Germany.

Department of Dermatology and Allergy Biederstein, Technical University of Munich, Biedersteiner Str. 29, 80802, Munich, Germany.

Institute of Human Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.

Institute of Human Genetics, Technical University of Munich, 81675, Munich, Germany.

University Clinic of Visceral Surgery and Medicine, Departement Klinische Forschung, University of Bern, Murtenstr. 35, CH-3010, Bern, Switzerland.

Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg.

Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, DK-5000, Odense C, Denmark.

Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Weihenstephan, Germany.

Center for Integrated Protein Science at the Department Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany. michael.groll@tum.de.

Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstr. 30, 81675, Munich, Germany. dirk.busch@tum.de.

Focus Group "Clinical Cell Processing and Purification", Institute for Advanced Study, Technical University of Munich, 81675, Munich, Germany. dirk.busch@tum.de.

German Center for Infection Research (DZIF), Trogerstr. 30, 81675, Munich, Germany. dirk.busch@tum.de.

Macromolecule Content

Total Structure Weight: 733.74 kDa
Atom Count: 49,853
Modeled Residue Count: 6,336
Deposited Residue Count: 6,614
Unique protein chains: 14

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	A, O	250	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23639 Go to UniProtKB: P23639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23639
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	B, P	258	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23638 Go to UniProtKB: P23638
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23638
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	C, Q	254	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40303 Go to UniProtKB: P40303
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40303
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	D, R	260	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32379 Go to UniProtKB: P32379
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32379
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	E, S	234	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40302 Go to UniProtKB: P40302
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40302
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable proteasome subunit alpha type-7	F, T	288	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21242 Go to UniProtKB: P21242
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21242
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	G, U	252	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21243 Go to UniProtKB: P21243
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21243
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	H, V	232	Saccharomyces cerevisiae S288C	Mutation(s): 1 EC: 3.4.25.1
UniProt
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25043 Go to UniProtKB: P25043
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25043
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	I, W	205	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25451 Go to UniProtKB: P25451
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25451
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Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	J, X	198	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22141 Go to UniProtKB: P22141
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22141
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	K, Y	212	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30656 Go to UniProtKB: P30656
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30656
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6	L, Z	222	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23724 Go to UniProtKB: P23724
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23724
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	AA [auth a], M	246	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30657 Go to UniProtKB: P30657
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30657
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	BA [auth b], N	196	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38624 Go to UniProtKB: P38624
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38624
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BO2 Query on BO2 Download:Ideal Coordinates CCD File SDF format, chain TA [auth b] SDF format, chain RA [auth Y] SDF format, chain QA [auth V] SDF format, chain MA [auth N] SDF format, chain JA [auth K] SDF format, chain EA [auth H] MOL2 format, chain TA [auth b] MOL2 format, chain RA [auth Y] MOL2 format, chain QA [auth V] MOL2 format, chain MA [auth N] MOL2 format, chain JA [auth K] MOL2 format, chain EA [auth H] mmCIF format, chain TA [auth b] mmCIF format, chain RA [auth Y] mmCIF format, chain QA [auth V] mmCIF format, chain MA [auth N] mmCIF format, chain JA [auth K] mmCIF format, chain EA [auth H]	EA [auth H] JA [auth K] MA [auth N] QA [auth V] RA [auth Y] EA [auth H], JA [auth K], MA [auth N], QA [auth V], RA [auth Y], TA [auth b]	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE C₁₉ H₂₅ B N₄ O₄ GXJABQQUPOEUTA-RDJZCZTQSA-N		Interactions Focus chain EA [auth H] Focus chain JA [auth K] Focus chain MA [auth N] Focus chain QA [auth V] Focus chain RA [auth Y] Focus chain TA [auth b] Interactions & Density Focus chain EA [auth H] Focus chain JA [auth K] Focus chain MA [auth N] Focus chain QA [auth V] Focus chain RA [auth Y] Focus chain TA [auth b]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain UA [auth b] SDF format, chain PA [auth U] SDF format, chain OA [auth N] SDF format, chain DA [auth G] MOL2 format, chain UA [auth b] MOL2 format, chain PA [auth U] MOL2 format, chain OA [auth N] MOL2 format, chain DA [auth G] mmCIF format, chain UA [auth b] mmCIF format, chain PA [auth U] mmCIF format, chain OA [auth N] mmCIF format, chain DA [auth G]	DA [auth G], OA [auth N], PA [auth U], UA [auth b]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth G] Focus chain OA [auth N] Focus chain PA [auth U] Focus chain UA [auth b] Interactions & Density Focus chain DA [auth G] Focus chain OA [auth N] Focus chain PA [auth U] Focus chain UA [auth b]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain SA [auth Z] SDF format, chain NA [auth N] SDF format, chain LA [auth L] SDF format, chain KA [auth K] SDF format, chain IA [auth J] SDF format, chain HA [auth I] SDF format, chain GA [auth I] SDF format, chain FA [auth H] SDF format, chain CA [auth G] MOL2 format, chain SA [auth Z] MOL2 format, chain NA [auth N] MOL2 format, chain LA [auth L] MOL2 format, chain KA [auth K] MOL2 format, chain IA [auth J] MOL2 format, chain HA [auth I] MOL2 format, chain GA [auth I] MOL2 format, chain FA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain SA [auth Z] mmCIF format, chain NA [auth N] mmCIF format, chain LA [auth L] mmCIF format, chain KA [auth K] mmCIF format, chain IA [auth J] mmCIF format, chain HA [auth I] mmCIF format, chain GA [auth I] mmCIF format, chain FA [auth H] mmCIF format, chain CA [auth G]	CA [auth G] FA [auth H] GA [auth I] HA [auth I] IA [auth J] CA [auth G], FA [auth H], GA [auth I], HA [auth I], IA [auth J], KA [auth K], LA [auth L], NA [auth N], SA [auth Z]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain LA [auth L] Focus chain NA [auth N] Focus chain SA [auth Z] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain KA [auth K] Focus chain LA [auth L] Focus chain NA [auth N] Focus chain SA [auth Z]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.218 (Depositor), 0.223 (DCC)
R-Value Work: 0.198 (Depositor), 0.203 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.22	α = 90
b = 300.86	β = 112.32
c = 144.1	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-06-15

Deposition Author(s):

Huber, E.M.

Groll, M.

Funding Organization	Location	Grant Number
German Research Foundation	Germany	GR1861/10-1
German Research Foundation	Germany	SFB1035/A2

Revision History (Full details and data files)

Version 1.0: 2016-06-15
Type: Initial release
Version 2.0: 2018-07-11
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations
Version 2.1: 2018-10-31
Changes: Data collection, Source and taxonomy, Structure summary
Version 2.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.3: 2024-11-06
Changes: Structure summary

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

5BXN | pdb_00005bxn

Yeast 20S proteasome beta2-G170A mutant in complex with Bortezomib

Literature

Defective immuno- and thymoproteasome assembly causes severe immunodeficiency.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)