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- PDB-3jrm: Crystal structure of archaeal 20S proteasome in complex with muta... -

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Basic information

Entry
Database: PDB / ID: 3jrm
TitleCrystal structure of archaeal 20S proteasome in complex with mutated P26 activator
Components
  • Proteasome activator protein PA26
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / 20S proteasome / PA26 / Cytoplasm / Hydrolase / Protease / Proteasome / Threonine protease / 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: 2.9 Å
AuthorsStadtmueller, B.M. / Whitby, F.G. / Hill, C.P.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural models for interactions between the 20S proteasome and its PAN/19S activators.
Authors: Stadtmueller, B.M. / Ferrell, K. / Whitby, F.G. / Heroux, A. / Robinson, H. / Myszka, D.G. / Hill, C.P.
History
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
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


Theoretical massNumber of molelcules
Total (without water)506,61721
Polymers506,61721
Non-polymers00
Water00
1
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
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

A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
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


Theoretical massNumber of molelcules
Total (without water)1,013,23442
Polymers1,013,23442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area181260 Å2
ΔGint-604.4 kcal/mol
Surface area308520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)255.075, 126.363, 180.781
Angle α, β, γ (deg.)90.00, 92.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
12H
22I
32J
42K
52L
62M
72N
13O
23P
33Q
43R
53S
63T
73U

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
11ALAALALEULEUAA7 - 2331 - 227
21ALAALALEULEUBB7 - 2331 - 227
31ALAALALEULEUCC7 - 2331 - 227
41ALAALALEULEUDD7 - 2331 - 227
51ALAALALEULEUEE7 - 2331 - 227
61ALAALALEULEUFF7 - 2331 - 227
71ALAALALEULEUGG7 - 2331 - 227
12THRTHRLEULEUHH1 - 2031 - 203
22THRTHRLEULEUII1 - 2031 - 203
32THRTHRLEULEUJJ1 - 2031 - 203
42THRTHRLEULEUKK1 - 2031 - 203
52THRTHRLEULEULL1 - 2031 - 203
62THRTHRLEULEUMM1 - 2031 - 203
72THRTHRLEULEUNN1 - 2031 - 203
13LYSLYSSERSEROO4 - 2311 - 228
23LYSLYSSERSERPP4 - 2311 - 228
33LYSLYSSERSERQQ4 - 2311 - 228
43LYSLYSSERSERRR4 - 2311 - 228
53LYSLYSSERSERSS4 - 2311 - 228
63LYSLYSSERSERTT4 - 2311 - 228
73LYSLYSSERSERUU4 - 2311 - 228

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 25125.619 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmA, Ta1288 / Production host: Escherichia coli (E. coli)
References: UniProt: P25156, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / Multicatalytic endopeptidase complex subunit beta


Mass: 22294.848 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmB, Ta0612 / Production host: Escherichia coli (E. coli)
References: UniProt: P28061, proteasome endopeptidase complex
#3: Protein
Proteasome activator protein PA26


Mass: 24953.369 Da / Num. of mol.: 7
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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: pH 5.6, PEG 1000, Sodium phosphate citrate, LiSo4, Imidazole, VAPOR DIFFUSION, Hanging Drop, temperature 294K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 126445 / % possible obs: 98.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.7
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.591 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YAR

1yar


Resolution: 2.9→29.82 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.906 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.502 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 2516 2 %RANDOM
Rwork0.20141 ---
obs0.20204 122666 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å2-2.77 Å2
2--1.08 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35035 0 0 0 35035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02235518
X-RAY DIFFRACTIONr_bond_other_d0.0020.0224038
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.97747971
X-RAY DIFFRACTIONr_angle_other_deg0.932358856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53654508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09224.3521512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.499156503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.22615245
X-RAY DIFFRACTIONr_chiral_restr0.0740.25607
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0239298
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026825
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.511.522435
X-RAY DIFFRACTIONr_mcbond_other0.0951.59282
X-RAY DIFFRACTIONr_mcangle_it1.047236092
X-RAY DIFFRACTIONr_scbond_it1.616313083
X-RAY DIFFRACTIONr_scangle_it2.9044.511879
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3003tight positional0.030.05
11B3003tight positional0.030.05
11C3003tight positional0.030.05
11D3003tight positional0.030.05
11E3003tight positional0.040.05
11F3003tight positional0.030.05
11G3003tight positional0.030.05
22A2611tight positional0.030.05
22B2611tight positional0.030.05
22C2611tight positional0.030.05
22D2611tight positional0.030.05
22E2611tight positional0.030.05
22F2611tight positional0.040.05
22G2611tight positional0.030.05
33A2827tight positional0.030.05
33B2827tight positional0.030.05
33C2827tight positional0.030.05
33D2827tight positional0.030.05
33E2827tight positional0.030.05
33F2827tight positional0.030.05
33G2827tight positional0.040.05
11A3003tight thermal0.060.5
11B3003tight thermal0.050.5
11C3003tight thermal0.060.5
11D3003tight thermal0.050.5
11E3003tight thermal0.060.5
11F3003tight thermal0.060.5
11G3003tight thermal0.060.5
22A2611tight thermal0.060.5
22B2611tight thermal0.060.5
22C2611tight thermal0.060.5
22D2611tight thermal0.060.5
22E2611tight thermal0.060.5
22F2611tight thermal0.070.5
22G2611tight thermal0.060.5
33A2827tight thermal0.060.5
33B2827tight thermal0.070.5
33C2827tight thermal0.060.5
33D2827tight thermal0.060.5
33E2827tight thermal0.070.5
33F2827tight thermal0.070.5
33G2827tight thermal0.070.5
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 172 -
Rwork0.293 8869 -
obs--98.14 %

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