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- PDB-2z5c: Crystal Structure of a Novel Chaperone Complex for Yeast 20S Prot... -

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Basic information

Entry
Database: PDB / ID: 2z5c
TitleCrystal Structure of a Novel Chaperone Complex for Yeast 20S Proteasome Assembly
Components
  • Proteasome component PUP2
  • Protein YPL144W
  • Uncharacterized protein YLR021W
KeywordsCHAPERONE/HYDROLASE / PROTEASOME / Chaperone / S. cerevisiae / CHAPERONE-HYDROLASE COMPLEX
Function / homology
Function and homology information


nuclear-transcribed mRNA catabolic process, non-stop decay / 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 ...nuclear-transcribed mRNA catabolic process, non-stop decay / 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 / chaperone-mediated protein complex assembly / proteasome assembly / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / Neutrophil degranulation / proteasome complex / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex / nucleus / cytoplasm
Similarity search - Function
Ribosomal Protein S5; domain 2 - #100 / Proteasome chaperone 3/4 / 20S proteasome chaperone assembly proteins 3 and 4 / Ribosomal Protein S5; domain 2 - #90 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Ribosomal Protein S5; domain 2 / Proteasome subunit alpha5 / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. ...Ribosomal Protein S5; domain 2 - #100 / Proteasome chaperone 3/4 / 20S proteasome chaperone assembly proteins 3 and 4 / Ribosomal Protein S5; domain 2 - #90 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Ribosomal Protein S5; domain 2 / Proteasome subunit alpha5 / 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 subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome subunit alpha type-5 / Proteasome chaperone 3 / Proteasome chaperone 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYashiroda, H. / Mizushima, T. / Okamoto, K. / Kameyama, T. / Hayashi, H. / Kishimoto, T. / Kasahara, M. / Kurimoto, E. / Sakata, E. / Suzuki, A. ...Yashiroda, H. / Mizushima, T. / Okamoto, K. / Kameyama, T. / Hayashi, H. / Kishimoto, T. / Kasahara, M. / Kurimoto, E. / Sakata, E. / Suzuki, A. / Hirano, Y. / Murata, S. / Kato, K. / Yamane, T. / Tanaka, K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes
Authors: Yashiroda, H. / Mizushima, T. / Okamoto, K. / Kameyama, T. / Hayashi, H. / Kishimoto, T. / Niwa, S. / Kasahara, M. / Kurimoto, E. / Sakata, E. / Takagi, K. / Suzuki, A. / Hirano, Y. / ...Authors: Yashiroda, H. / Mizushima, T. / Okamoto, K. / Kameyama, T. / Hayashi, H. / Kishimoto, T. / Niwa, S. / Kasahara, M. / Kurimoto, E. / Sakata, E. / Takagi, K. / Suzuki, A. / Hirano, Y. / Murata, S. / Kato, K. / Yamane, T. / Tanaka, K.
History
DepositionJul 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.3Nov 1, 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein YPL144W
B: Uncharacterized protein YLR021W
C: Proteasome component PUP2
D: Protein YPL144W
E: Uncharacterized protein YLR021W
F: Proteasome component PUP2


Theoretical massNumber of molelcules
Total (without water)124,9806
Polymers124,9806
Non-polymers00
Water00
1
A: Protein YPL144W
B: Uncharacterized protein YLR021W
C: Proteasome component PUP2


Theoretical massNumber of molelcules
Total (without water)62,4903
Polymers62,4903
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-18 kcal/mol
Surface area19690 Å2
MethodPISA
2
D: Protein YPL144W
E: Uncharacterized protein YLR021W
F: Proteasome component PUP2


Theoretical massNumber of molelcules
Total (without water)62,4903
Polymers62,4903
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-17.8 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.687, 159.181, 65.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLYGLYAA4 - 1477 - 150
21LYSLYSGLYGLYDD4 - 1477 - 150
12ILEILEALAALABB2 - 1782 - 148
22ILEILEALAALAEE2 - 1782 - 148
13LEULEUGLUGLUCC33 - 25035 - 252
23LEULEUGLUGLUFF33 - 25035 - 252

NCS ensembles :
ID
1
2
3
Detailsthe biological unit for Dmp1 and Dmp2 is hetero dimer. In this entry, the quaternary assembly is a hetero trimer - Dmp1 and Dmp2 complexed with a part of the 20S proteasome, proteasome subunit alpha 5

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Components

#1: Protein Protein YPL144W / Dmp1


Mass: 16876.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12245
#2: Protein Uncharacterized protein YLR021W / Dmp2


Mass: 16820.182 Da / Num. of mol.: 2 / Fragment: UNP residues 1-60, 91-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07951
#3: Protein Proteasome component PUP2 / Macropain subunit PUP2 / Proteinase YSCE subunit PUP2 / Multicatalytic endopeptidase complex ...Macropain subunit PUP2 / Proteinase YSCE subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / proteasome subunit alpha 5


Mass: 28793.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P32379, proteasome endopeptidase complex

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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: 3.29 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 8%(v/v) ethyleneglycol, 12%(w/v) PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Apr 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50.38 Å / Num. obs: 37091 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.35 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z5B; PDB ENTRY 1RYP chain E

2z5b

1ryp


Resolution: 2.9→50.38 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.875 / SU B: 14.479 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 0.641 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28334 1859 5 %RANDOM
Rwork0.24962 ---
obs0.2513 35178 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.851 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2--2.45 Å20 Å2
3----5.06 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6598 0 0 0 6598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226688
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.989006
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8465810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34124.755286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.623151252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9181534
X-RAY DIFFRACTIONr_chiral_restr0.1150.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024816
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.23224
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.24432
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4020.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3630.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.91.54271
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60226692
X-RAY DIFFRACTIONr_scbond_it1.63432717
X-RAY DIFFRACTIONr_scangle_it2.6934.52314
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A981tight positional0.030.05
2B857tight positional0.010.05
3C1464tight positional0.010.05
1A981tight thermal0.040.5
2B857tight thermal0.020.5
3C1464tight thermal0.030.5
LS refinement shellResolution: 2.904→2.979 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 124 -
Rwork0.34 2455 -
obs--94.99 %

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