5BXL

Yeast 20S proteasome beta2-G170A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • DOI: 10.1038/s41598-018-24199-0
  • Primary Citation of Related Structures:  

  • 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. ...

    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

    German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Focus Group "Clinical Cell Processing and Purification", Institute for Advanced Study, Technical University of Munich, 81675, Munich, Germany. dirk.busch@tum.de.,Division of Immunology, Department of Biology, University of Konstanz, Universitaetsstr. 10, 78457, Konstanz, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Weihenstephan, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstr. 30, 81675, Munich, Germany. dirk.busch@tum.de.,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.,Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, L-4354, Esch-sur-Alzette, Luxembourg.,German Center for Diabetes Research (DZD), Ingostädter Landstr. 1, 85764, Neuherberg, Germany.,Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, DK-5000, Odense C, Denmark.,German Center for Infection Research (DZIF), Trogerstr. 30, 81675, Munich, Germany. dirk.busch@tum.de.,Institute of Pathology, 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.,University Clinic of Visceral Surgery and Medicine, Departement Klinische Forschung, University of Bern, Murtenstr. 35, CH-3010, Bern, Switzerland.,Institute of Human Genetics, Technical University of Munich, 81675, Munich, Germany.,Institute for Molecular Animal Breeding and Biotechnology, Gene Center of the Ludwig-Maximilians-Universität München, Feodor-Lynen Str. 25, 81377, Munich, Germany.,Department of Dermatology and Allergy Biederstein, Technical University of Munich, Biedersteiner Str. 29, 80802, Munich, Germany.,Institute for Medical Microbiology, Immunology and Hygiene, Technical University of Munich, Trogerstr. 30, 81675, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
A, O
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE8 (PRS4)
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
B, P
258Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE9 (PRS5)
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
C, Q
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE6
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
D, R
260Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP2 (DOA5)
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
E, S
234Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE5
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40302
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Probable proteasome subunit alpha type-7
F, T
288Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE10 (PRC1, PRS1)
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21242
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
G, U
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SCL1 (PRC2, PRS2)
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
H, V
232Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP1
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25043
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
I, W
205Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP3
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25451
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
J, X
198Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE1
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
K, Y
212Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE2 (DOA3, PRG1)
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30656
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
L, Z
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE7 (PRS3, PTS1)
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23724
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
M, a
246Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE4
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
N, b
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE3
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
G, U
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
G, H, I, K, L, N, W, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 134.800α = 90.00
b = 300.940β = 112.71
c = 144.490γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
XSCALEdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-06-09 
  • Released Date: 2016-06-15 
  • Deposition Author(s): Huber, E.M., Groll, M.

Funding OrganizationLocationGrant Number
German Research FoundationGermanyGR1861/10-1
German Research FoundationGermanySFB1035/A2

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2018-07-11
    Type: Author supporting evidence, Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Advisory, Data collection, Derived calculations