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- PDB-1z7q: Crystal structure of the 20s proteasome from yeast in complex wit... -

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Basic information

Entry
Database: PDB / ID: 1z7q
TitleCrystal structure of the 20s proteasome from yeast in complex with the proteasome activator PA26 from Trypanosome brucei at 3.2 angstroms resolution
Components
  • (Proteasome component ...) x 13
  • Potential proteasome component C5
  • proteasome activator protein PA26
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / 20S / proteasome / PA26 / activator / multi-catalytic protease / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX
Function / homology
Function and homology information


proteasome activator complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly ...proteasome activator complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / proteolysis / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome activator pa28, C-terminal domain / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator pa28 beta subunit / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 ...Proteasome activator pa28, C-terminal domain / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator pa28 beta subunit / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 4-Layer Sandwich / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 ...Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / Proteasome activator protein PA26
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Trypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å
AuthorsForster, A. / Whitby, F.G. / Hill, C.P.
CitationJournal: Mol.Cell / Year: 2005
Title: The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions.
Authors: Forster, A. / Masters, E.I. / Whitby, F.G. / Robinson, H. / Hill, C.P.
History
DepositionMar 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 3, 2014Group: Other
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 999SEQUENCE Residue (i GLY 1172) and Residue (i GLY 1173) are not linked. Distance of C-N bond is 1.91. ...SEQUENCE Residue (i GLY 1172) and Residue (i GLY 1173) are not linked. Distance of C-N bond is 1.91. Residue (p GLY 1172) and Residue (p GLY 1173) are not linked. Distance of C-N bond is 1.91.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome component C7-alpha
B: Proteasome component Y7
C: Proteasome component Y13
D: Proteasome component PRE6
E: Proteasome component PUP2
F: Proteasome component PRE5
G: Proteasome component C1
H: Proteasome component PRE3
I: Proteasome component PUP1
J: Proteasome component PUP3
K: Proteasome component C11
L: Proteasome component PRE2
M: Potential proteasome component C5
N: Proteasome component PRE4
O: Proteasome component C7-alpha
P: Proteasome component Y7
Q: Proteasome component Y13
R: Proteasome component PRE6
S: Proteasome component PUP2
T: Proteasome component PRE5
U: Proteasome component C1
V: Proteasome component PRE3
W: Proteasome component PUP1
X: Proteasome component PUP3
Y: Proteasome component C11
Z: Proteasome component PRE2
a: Potential proteasome component C5
b: Proteasome component PRE4
c: proteasome activator protein PA26
d: proteasome activator protein PA26
e: proteasome activator protein PA26
f: proteasome activator protein PA26
g: proteasome activator protein PA26
h: proteasome activator protein PA26
i: proteasome activator protein PA26
j: proteasome activator protein PA26
k: proteasome activator protein PA26
l: proteasome activator protein PA26
m: proteasome activator protein PA26
n: proteasome activator protein PA26
o: proteasome activator protein PA26
p: proteasome activator protein PA26


Theoretical massNumber of molelcules
Total (without water)1,079,54442
Polymers1,079,54442
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)192.964, 232.127, 296.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details1 complete, 28-subunit 20S proteasome is found in the asymmetric unit / 2 complete, 7-subunit PA26 compllexes are found in the asymmetric unit

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Components

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Proteasome component ... , 13 types, 26 molecules AOBPCQDRESFTGUHVIWJXKYLZNb

#1: Protein Proteasome component C7-alpha / / Macropain subunit C7- alpha / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex C7 / ...Macropain subunit C7- alpha / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex C7 / Component Y8 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P21243, proteasome endopeptidase complex
#2: Protein Proteasome component Y7 / / Macropain subunit Y7 / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex subunit Y7


Mass: 27191.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23639, proteasome endopeptidase complex
#3: Protein Proteasome component Y13 / / Macropain subunit Y13 / Proteinase YSCE subunit 13 / Multicatalytic endopeptidase complex subunit Y13


Mass: 28748.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23638, proteasome endopeptidase complex
#4: Protein Proteasome component PRE6 / / Macropain subunit PRE6 / Proteinase YSCE subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P40303, proteasome endopeptidase complex
#5: Protein Proteasome component PUP2 / / Macropain subunit PUP2 / Proteinase YSCE subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P32379, proteasome endopeptidase complex
#6: Protein Proteasome component PRE5 / / Macropain subunit PRE5 / Proteinase YSCE subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P40302, proteasome endopeptidase complex
#7: Protein Proteasome component C1 / / Macropain subunit C1 / Proteinase YSCE subunit 1 / Multicatalytic endopeptidase complex subunit C1


Mass: 31575.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P21242, proteasome endopeptidase complex
#8: Protein Proteasome component PRE3 / / Macropain subunit PRE3 / Proteinase YSCE subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P38624, proteasome endopeptidase complex
#9: Protein Proteasome component PUP1 / / Macropain subunit PUP1 / Proteinase YSCE subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1


Mass: 23987.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#10: Protein Proteasome component PUP3 / / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3


Mass: 22627.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25451, proteasome endopeptidase complex
#11: Protein Proteasome component C11 / / Macropain subunit C11 / Proteinase YSCE subunit 11 / Multicatalytic endopeptidase complex subunit C11


Mass: 22545.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#12: Protein Proteasome component PRE2 / / Macropain subunit PRE2 / Proteinase YSCE subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2


Mass: 23353.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#14: Protein Proteasome component PRE4 / / Macropain subunit PRE4 / Proteinase YSCE subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4


Mass: 25945.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P30657, proteasome endopeptidase complex

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Protein , 2 types, 16 molecules Macdefghijklmnop

#13: Protein Potential proteasome component C5 / Multicatalytic endopeptidase complex subunit C5


Mass: 24883.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23724, proteasome endopeptidase complex
#15: Protein
proteasome activator protein PA26


Mass: 25228.734 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U8G2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M NaHEPES, 40% MPD, 0.2 M NACL, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000
RadiationMonochromator: SSRL beamline 9-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 189615 / Num. obs: 189615 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 7
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.331 / % possible all: 0.0629

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: one-half of the yeast 20S proteasome (Huber, et al., high-resolution structure), pdb entry 1RYP

1ryp


Resolution: 3.22→39.8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1264 -random
Rwork0.263 ---
obs0.263 189495 89.1 %-
all-189615 --
Refinement stepCycle: LAST / Resolution: 3.22→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms74222 0 0 0 74222

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