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- PDB-1yar: Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex -

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Basic information

Entry
Database: PDB / ID: 1yar
TitleStructure of Archeabacterial 20S proteasome mutant D9S- PA26 complex
Components
  • Proteasome alpha subunit
  • Proteasome beta subunit
  • proteasome activator protein PA26
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / proteasome 20S / PA26 proteasome activator 11S / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX
Function / homology
Function and homology information


proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / regulation of proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteolysis / 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, C-terminal / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta-type subunits signature. ...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 / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 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
: / Proteasome subunit alpha / Proteasome subunit beta / Proteasome activator protein PA26
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
Trypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsForster, A. / Masters, E.I. / Whitby, F.G. / Robinson, H. / 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
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_ref_seq_dif ...database_2 / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE For the Proteasome beta subunit (chains H,I,J,K,L,M,N) the first 8 residues are cleaved ...SEQUENCE For the Proteasome beta subunit (chains H,I,J,K,L,M,N) the first 8 residues are cleaved off autocatalytically during assembly of the complex.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome alpha subunit
B: Proteasome alpha subunit
C: Proteasome alpha subunit
D: Proteasome alpha subunit
E: Proteasome alpha subunit
F: Proteasome alpha subunit
G: Proteasome alpha subunit
H: Proteasome beta subunit
I: Proteasome beta subunit
J: Proteasome beta subunit
K: Proteasome beta subunit
L: Proteasome beta subunit
M: Proteasome beta subunit
N: Proteasome beta subunit
O: proteasome activator protein PA26
P: proteasome activator protein PA26
Q: proteasome activator protein PA26
R: proteasome activator protein PA26
S: proteasome activator protein PA26
T: proteasome activator protein PA26
U: proteasome activator protein PA26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,87649
Polymers531,21421
Non-polymers2,66228
Water62,5123470
1
A: Proteasome alpha subunit
B: Proteasome alpha subunit
C: Proteasome alpha subunit
D: Proteasome alpha subunit
E: Proteasome alpha subunit
F: Proteasome alpha subunit
G: Proteasome alpha subunit
H: Proteasome beta subunit
I: Proteasome beta subunit
J: Proteasome beta subunit
K: Proteasome beta subunit
L: Proteasome beta subunit
M: Proteasome beta subunit
N: Proteasome beta subunit
O: proteasome activator protein PA26
P: proteasome activator protein PA26
Q: proteasome activator protein PA26
R: proteasome activator protein PA26
S: proteasome activator protein PA26
T: proteasome activator protein PA26
U: proteasome activator protein PA26
hetero molecules

A: Proteasome alpha subunit
B: Proteasome alpha subunit
C: Proteasome alpha subunit
D: Proteasome alpha subunit
E: Proteasome alpha subunit
F: Proteasome alpha subunit
G: Proteasome alpha subunit
H: Proteasome beta subunit
I: Proteasome beta subunit
J: Proteasome beta subunit
K: Proteasome beta subunit
L: Proteasome beta subunit
M: Proteasome beta subunit
N: Proteasome beta subunit
O: proteasome activator protein PA26
P: proteasome activator protein PA26
Q: proteasome activator protein PA26
R: proteasome activator protein PA26
S: proteasome activator protein PA26
T: proteasome activator protein PA26
U: proteasome activator protein PA26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,067,75398
Polymers1,062,42942
Non-polymers5,32456
Water75742
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area191730 Å2
ΔGint-1284 kcal/mol
Surface area308320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)254.874, 127.512, 181.182
Angle α, β, γ (deg.)90.00, 92.45, 90.00
Int Tables number5
Space group name H-MC121
DetailsT. acidophilum is a 28-subunit barrel-shaped complex. It contains 2 stacked homoheptameric rings of beta subunits flanked by 2 homoheptameric rings of alpha subunits. One half of the 20S complex is contained in the asymmetric unit (one ring of beta and one ring of alpha subunits. / PA26 is a homoheptameric ring that binds to the end of the 20S proteasome through interactions with the 20S alpha subunits. One PA26 complex is contained in the asymmetric unit.

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Components

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Protein , 3 types, 21 molecules ABCDEFGHIJKLMNOPQRSTU

#1: Protein
Proteasome alpha subunit / Multicatalytic endopeptidase complex alpha subunit


Mass: 25801.439 Da / Num. of mol.: 7 / Mutation: D9S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmA / Plasmid: pRSET5a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P25156, proteasome endopeptidase complex
#2: Protein
Proteasome beta subunit / Multicatalytic endopeptidase complex beta subunit


Mass: 23998.691 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmB / Plasmid: pRSET5a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P28061, proteasome endopeptidase complex
#3: Protein
proteasome activator protein PA26


Mass: 26087.643 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Plasmid: pBTpa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 5757773, UniProt: Q9U8G2*PLUS

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Non-polymers , 3 types, 3498 molecules

#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3470 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M Na-citrate/phosphate buffer, 0.2M Lithium Sulfate, 15% PEG-1000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.283 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 442007 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 10
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.2 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PMA

1pma


Resolution: 1.9→47.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.843 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.131 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21624 1345 0.3 %RANDOM
Rwork0.18185 ---
all0.18196 442001 --
obs0.18196 440656 97.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.532 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34692 0 147 3470 38309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02236741
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.96949874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80754792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6924.4341547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.644156748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.90315252
X-RAY DIFFRACTIONr_chiral_restr0.0920.25763
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0227442
X-RAY DIFFRACTIONr_nbd_refined0.2090.219081
X-RAY DIFFRACTIONr_nbtor_refined0.30.226212
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.23514
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.2147
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.263
X-RAY DIFFRACTIONr_mcbond_it0.9731.524072
X-RAY DIFFRACTIONr_mcangle_it1.51237633
X-RAY DIFFRACTIONr_scbond_it2.472314351
X-RAY DIFFRACTIONr_scangle_it3.8984.512241
LS refinement shellResolution: 1.899→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 85 -
Rwork0.237 31236 -
obs--93.61 %

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