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- PDB-1fnt: CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST IN COMPLEX WIT... -

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Entry
Database: PDB / ID: 1fnt
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 14
  • PROTEASOME ACTIVATOR PROTEIN PA26
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / MULTICATALYTIC PROTEINASE / 20S PROTEASOME / PROTEIN DEGRADATION / ANTIGEN PROCESSING / PROTEASE / PROTEASOME ACTIVATOR / CELL ADHESION / INTERFERON INDUCTION / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX
Function / homology
Function and homology information


proteasome activator complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 ...proteasome activator complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / Ub-specific processing proteases / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / regulation of proteasomal protein catabolic process / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / proteolysis / nucleus / cytosol
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, C-terminal / 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, C-terminal / 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 alpha5 / Proteasome subunit alpha6 / 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 B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-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: 3.2 Å
AuthorsWhitby, F.G. / Masters, E. / Kramer, L. / Knowlton, J.R. / Yao, Y. / Wang, C.C. / Hill, C.P.
CitationJournal: Nature / Year: 2000
Title: Structural basis for the activation of 20S proteasomes by 11S regulators.
Authors: Whitby, F.G. / Masters, E.I. / Kramer, L. / Knowlton, J.R. / Yao, Y. / Wang, C.C. / Hill, C.P.
History
DepositionAug 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 42 CHAIN(S). SEE REMARK ... THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 42 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). YEAST PROTEASOME IS COMPOSED OF 14 DIFFERENT SUBUNITS WHICH FORM A HIGHLY ORDERED RING-SHAPED STRUCTURE. PA26 IS A HEPTAMER.

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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: 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,079,36056
Polymers1,079,01942
Non-polymers34014
Water00
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

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Components

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PROTEASOME COMPONENT ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZMaNb

#1: Protein PROTEASOME COMPONENT C7-ALPHA


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, EC: 3.4.99.46
#2: Protein PROTEASOME COMPONENT 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, EC: 3.4.99.46
#3: Protein PROTEASOME COMPONENT Y13


Mass: 27181.609 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, EC: 3.4.99.46
#4: Protein PROTEASOME COMPONENT 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, EC: 3.4.99.46
#5: Protein PROTEASOME COMPONENT 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, EC: 3.4.99.46
#6: Protein PROTEASOME COMPONENT 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, EC: 3.4.99.46
#7: Protein PROTEASOME COMPONENT C1


Mass: 31443.875 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, EC: 3.4.99.46
#8: Protein PROTEASOME COMPONENT 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, EC: 3.4.99.46
#9: Protein PROTEASOME COMPONENT PUP1


Mass: 25114.459 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, EC: 3.4.99.46
#10: Protein PROTEASOME COMPONENT 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, EC: 3.4.99.46
#11: Protein PROTEASOME COMPONENT 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, EC: 3.4.99.46
#12: Protein PROTEASOME COMPONENT 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, EC: 3.4.99.46
#13: Protein PROTEASOME COMPONENT 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, EC: 3.4.99.46
#14: Protein PROTEASOME COMPONENT 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, EC: 3.4.99.46

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Protein / Non-polymers , 2 types, 28 molecules cdefghijklmnop

#15: Protein
PROTEASOME ACTIVATOR PROTEIN PA26


Mass: 25272.787 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
#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg

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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: 60.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M NaHEPES, 40% MPD, 0.2 M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
21 mMEDTA1drop
31 mMdithiothreitol1drop
410 mg/mlprotein1drop
50.1 Msodium HEPES1reservoir
640 %MPD1reservoir
70.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2000 / Details: SSRL/9-1
RadiationMonochromator: SSRL/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. obs: 189495 / % possible obs: 89.1 % / 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: 62.9
Reflection
*PLUS
Num. measured all: 503540
Reflection shell
*PLUS
% possible obs: 62.9 % / Num. unique obs: 6632 / Num. measured obs: 16790

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Processing

Software
NameVersionClassification
AMoREphasing
CCP4model building
DMmodel building
RAVEmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
DMphasing
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1/2 OF 20S PROTEASOME INCLUDING ALPHA-1-7 AND REMARK 200 BETA-1-7, REDUCED TO A POLY-ALANINE MODEL.

Resolution: 3.2→50 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: NCS RESTRAINTS APPLIED CONSIDERING THE 14-FOLD SYMMETRY OF PA26 IN THE ASYMMETRIC UNIT AND THE 2-FOLD SYMMETRY OF 20S PROTEASOME
RfactorNum. reflection% reflectionSelection details
Rfree0.325 1028 0.5 %RANDOM
Rwork0.255 ---
obs0.255 189495 86.6 %-
Displacement parametersBiso mean: 83 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--1.2 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.5 Å
Luzzati sigma a0.69 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms70608 0 14 0 70622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.77
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3.2→3.35 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.404 65 0.5 %
Rwork0.376 13432 -
obs--49.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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