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- PDB-3dy4: Crystal structure of yeast 20S proteasome in complex with spirola... -

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Basic information

Entry
Database: PDB / ID: 3dy4
TitleCrystal structure of yeast 20S proteasome in complex with spirolactacystin
Components(Proteasome component ...) x 14
KeywordsHYDROLASE / Proteasome / Inhibitor / Protein Degradation / Ubiquitin-Proteasome-Pathway / Nucleus / Protease / Threonine protease / Phosphoprotein / Zymogen
Function / homology
Function and homology information


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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation ...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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / peroxisome / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol
Similarity search - Function
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. ...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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Omuralide, open form / 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 ...Omuralide, open form / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsGroll, M. / Balskus, E. / Jacobsen, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Structural analysis of spiro beta-lactone proteasome inhibitors.
Authors: Groll, M. / Balskus, E.P. / Jacobsen, E.N.
History
DepositionJul 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 13, 2014Group: Non-polymer description
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome component Y7
B: Proteasome component Y13
C: Proteasome component PRE6
D: Proteasome component PUP2
E: Proteasome component PRE5
F: Proteasome component C1
G: Proteasome component C7-alpha
H: Proteasome component PUP1
I: Proteasome component PUP3
J: Proteasome component C11
K: Proteasome component PRE2
L: Proteasome component C5
M: Proteasome component PRE4
N: Proteasome component PRE3
O: Proteasome component Y7
P: Proteasome component Y13
Q: Proteasome component PRE6
R: Proteasome component PUP2
S: Proteasome component PRE5
T: Proteasome component C1
U: Proteasome component C7-alpha
V: Proteasome component PUP1
W: Proteasome component PUP3
X: Proteasome component C11
Y: Proteasome component PRE2
Z: Proteasome component C5
1: Proteasome component PRE4
2: Proteasome component PRE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)705,06732
Polymers704,20628
Non-polymers8614
Water17,655980
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area115450 Å2
ΔGint-351.4 kcal/mol
Surface area214070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.160, 301.973, 144.050
Angle α, β, γ (deg.)90.00, 112.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Proteasome component ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZM1N2

#1: 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 natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein Proteasome component Y13 / Macropain subunit Y13 / Proteinase YSCE subunit 13 / Multicatalytic endopeptidase complex subunit Y13


Mass: 27050.416 Da / Num. of mol.: 2 / Fragment: UNP residues 2-245 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein Proteasome component PRE6 / Macropain subunit PRE6 / Proteinase YSCE subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6


Mass: 26903.330 Da / Num. of mol.: 2 / Fragment: UNP residues 3-243 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome component PUP2 / Macropain subunit PUP2 / Proteinase YSCE subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2


Mass: 26544.789 Da / Num. of mol.: 2 / Fragment: UNP residues 9-250 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein Proteasome component PRE5 / Macropain subunit PRE5 / Proteinase YSCE subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5


Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P40302, proteasome endopeptidase complex
#6: Protein Proteasome component C1 / Macropain subunit C1 / Proteinase YSCE subunit 1 / Multicatalytic endopeptidase complex subunit C1


Mass: 26892.482 Da / Num. of mol.: 2 / Fragment: UNP residues 5-248 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P21242, proteasome endopeptidase complex
#7: 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 / Proteasome component Y8 / SCL1 suppressor protein


Mass: 27316.037 Da / Num. of mol.: 2 / Fragment: UNP residues 10-252 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P21243, proteasome endopeptidase complex
#8: Protein Proteasome component PUP1 / Macropain subunit PUP1 / Proteinase YSCE subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1


Mass: 23987.254 Da / Num. of mol.: 2 / Fragment: UNP residues 30-251 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome component PUP3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3


Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P25451, proteasome endopeptidase complex
#10: 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 natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome component PRE2 / Macropain subunit PRE2 / Proteinase YSCE subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2


Mass: 23325.248 Da / Num. of mol.: 2 / Fragment: UNP residues 76-287 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome component C5 / Multicatalytic endopeptidase complex subunit C5


Mass: 24883.928 Da / Num. of mol.: 2 / Fragment: UNP residues 20-241 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome component PRE4 / Macropain subunit PRE4 / Proteinase YSCE subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4


Mass: 25945.496 Da / Num. of mol.: 2 / Fragment: UNP residues 34-266 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome component PRE3 / Macropain subunit PRE3 / Proteinase YSCE subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Fragment: UNP residues 20-215 / Source method: isolated from a natural source
Details: 20S proteasome was prepared from yeast under native conditions
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cell line: native purification
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 2 types, 984 molecules

#15: Chemical
ChemComp-SLA / Omuralide, open form / (2R,3S,4R)-3-hydroxy-2-[(1S)-1-hydroxy-2-methylpropyl]-4-methyl-5-oxopyrrolidine-2-carbaldehyde


Mass: 215.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17NO4 / Details: Spirolactacystin prepared by chemical synthesis
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 980 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsSPIROLACTASYSTIN IS COVALENTLY BOUND TO THR1 OF SUBUNITS BETA1, BETA2 AND BETA5 BY ESTER BOND FORMATION.
Sequence detailsPROTEASOME IS COMPOSED OF 28 SUBUNITS: ALPHA(1-7)-BETA(1-7)-BETA(1-7)-ALPHA(1-7)

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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: 3.85 Å3/Da / Density % sol: 68.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M MES, 10 % MPD, 20 mM MgAc2, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2007
RadiationMonochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→99 Å / Num. all: 259827 / Num. obs: 254111 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.142
Reflection shellResolution: 2.8→2.81 Å / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 1.9 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata scaling
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1RYP

1ryp


Resolution: 2.8→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3377439.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 12620 5 %RANDOM
Rwork0.227 ---
all0.228 254111 --
obs0.227 253087 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.0638 Å2 / ksol: 0.353509 e/Å3
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1-17.88 Å20 Å2-2.45 Å2
2---26.07 Å20 Å2
3---8.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49548 0 60 980 50588
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 2142 5 %
Rwork0.345 40364 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramsl.top
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4sl.par

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