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

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Basic information

Entry
Database: PDB / ID: 3jtl
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 / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteolysis ...proteasome activator complex / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / endopeptidase activity / proteolysis / cytoplasm / 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 / 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 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 / 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: 3.2 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 12, 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)507,76721
Polymers507,76721
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)1,015,53342
Polymers1,015,53342
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area188970 Å2
ΔGint-653 kcal/mol
Surface area310830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)255.826, 126.582, 182.170
Angle α, β, γ (deg.)90.000, 92.950, 90.000
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
13LYSLYSARGARGOO4 - 2311 - 228
23LYSLYSARGARGPP4 - 2311 - 228
33LYSLYSARGARGQQ4 - 2311 - 228
43LYSLYSARGARGRR4 - 2311 - 228
53LYSLYSARGARGSS4 - 2311 - 228
63LYSLYSARGARGTT4 - 2311 - 228
73LYSLYSARGARGUU4 - 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 / Fragment: Alpha subunit
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 / Fragment: Beta subunit
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: 25117.617 Da / Num. of mol.: 7 / Fragment: PA26 with mutations in tail
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 / 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
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 95561 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.257 / Net I/σ(I): 4.2
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.642 / % possible all: 90.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YAR

1yar


Resolution: 3.2→29.85 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.891 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.057 / SU ML: 0.313 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.449 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1905 2 %RANDOM
Rwork0.194 ---
obs0.195 94901 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.17 Å2
2---0.21 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35140 0 0 0 35140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02235600
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.97848085
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88754508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26624.3151525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.661156536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.91515252
X-RAY DIFFRACTIONr_chiral_restr0.0950.25627
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02126187
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5271.522442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.082236117
X-RAY DIFFRACTIONr_scbond_it1.703313158
X-RAY DIFFRACTIONr_scangle_it3.0994.511968
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
11A1751tight positional0.050.05
12B1751tight positional0.040.05
13C1751tight positional0.040.05
14D1751tight positional0.040.05
15E1751tight positional0.050.05
16F1751tight positional0.050.05
17G1751tight positional0.040.05
21H1557tight positional0.040.05
22I1557tight positional0.040.05
23J1557tight positional0.040.05
24K1557tight positional0.040.05
25L1557tight positional0.040.05
26M1557tight positional0.050.05
27N1557tight positional0.040.05
31O1687tight positional0.040.05
32P1687tight positional0.040.05
33Q1687tight positional0.040.05
34R1687tight positional0.050.05
35S1687tight positional0.050.05
36T1687tight positional0.050.05
37U1687tight positional0.050.05
11A1751tight thermal0.060.5
12B1751tight thermal0.060.5
13C1751tight thermal0.060.5
14D1751tight thermal0.060.5
15E1751tight thermal0.070.5
16F1751tight thermal0.060.5
17G1751tight thermal0.070.5
21H1557tight thermal0.070.5
22I1557tight thermal0.060.5
23J1557tight thermal0.070.5
24K1557tight thermal0.070.5
25L1557tight thermal0.070.5
26M1557tight thermal0.070.5
27N1557tight thermal0.070.5
31O1687tight thermal0.060.5
32P1687tight thermal0.070.5
33Q1687tight thermal0.070.5
34R1687tight thermal0.070.5
35S1687tight thermal0.070.5
36T1687tight thermal0.070.5
37U1687tight thermal0.070.5
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 143 -
Rwork0.303 6189 -
obs--90.51 %

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