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- PDB-1avo: PROTEASOME ACTIVATOR REG(ALPHA) -

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Basic information

Entry
Database: PDB / ID: 1avo
TitlePROTEASOME ACTIVATOR REG(ALPHA)
Components(11S REGULATOR) x 2
KeywordsPROTEASOME ACTIVATOR / CELL ADHESION / INTERFERON INDUCTION
Function / homology
Function and homology information


proteasome activator complex / antigen processing and presentation of exogenous antigen / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / regulation of G1/S transition of mitotic cell cycle / endopeptidase activator activity / regulation of proteasomal protein catabolic process / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation ...proteasome activator complex / antigen processing and presentation of exogenous antigen / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / regulation of G1/S transition of mitotic cell cycle / endopeptidase activator activity / regulation of proteasomal protein catabolic process / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / Ub-specific processing proteases / extracellular exosome / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Proteasome activator pa28, N-terminal domain / Proteasome activator pa28, C-terminal domain / Proteasome activator PA28, N-terminal domain / Proteasome activator PA28, N-terminal domain superfamily / Proteasome activator pa28 alpha subunit / Proteasome activator PA28 / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator pa28 beta subunit ...Proteasome activator pa28, N-terminal domain / Proteasome activator pa28, C-terminal domain / Proteasome activator PA28, N-terminal domain / Proteasome activator PA28, N-terminal domain superfamily / Proteasome activator pa28 alpha subunit / Proteasome activator PA28 / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator pa28 beta subunit / Four Helix Bundle (Hemerythrin (Met), subunit A) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Proteasome activator complex subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR/AVERAGING / Resolution: 2.8 Å
AuthorsHill, C.P. / Knowlton, J.R.
CitationJournal: Nature / Year: 1997
Title: Structure of the proteasome activator REGalpha (PA28alpha).
Authors: Knowlton, J.R. / Johnston, S.C. / Whitby, F.G. / Realini, C. / Zhang, Z. / Rechsteiner, M. / Hill, C.P.
History
DepositionSep 18, 1997Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 11S REGULATOR
B: 11S REGULATOR
C: 11S REGULATOR
D: 11S REGULATOR
E: 11S REGULATOR
F: 11S REGULATOR
G: 11S REGULATOR
H: 11S REGULATOR
I: 11S REGULATOR
J: 11S REGULATOR
K: 11S REGULATOR
L: 11S REGULATOR
M: 11S REGULATOR
N: 11S REGULATOR


Theoretical massNumber of molelcules
Total (without water)161,50814
Polymers161,50814
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52180 Å2
ΔGint-304 kcal/mol
Surface area55860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.600, 134.300, 116.200
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
11S REGULATOR / REG(ALPHA) / PA28(ALPHA)


Mass: 6753.724 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: PAED4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q06323
#2: Protein
11S REGULATOR / REG(ALPHA) / PA28(ALPHA)


Mass: 16318.890 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: PAED4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q06323

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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: 3.93 Å3/Da / Density % sol: 68.67 %
Crystal growpH: 7.1 / Details: pH 7.1
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
25 mMMops1drop
30.1 mMEDTA1drop
40.5 mMdithiothreitol1drop
56 %PEG60001drop
650 mMNa-MOPS1drop
71 M1dropNaCl
80.45 mM1dropZnCl2
912 %PEG60001reservoir
10100 mMNa-MOPS1reservoir
112 M1reservoirNaCl
120.9 mM1reservoirZnCl2

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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 1, 1997 / Details: SSRL/9-1
RadiationMonochromator: SSRL/9-1 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 32245 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 17
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 9 / Rsym value: 0.241 / % possible all: 95
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR/AVERAGING / Resolution: 2.8→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1467 2.5 %RANDOM
Rwork0.249 ---
obs0.249 32245 98.4 %-
Displacement parametersBiso mean: 28.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13958 0 0 0 13958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 2.8→2.85 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4 153 2.2 %
Rwork0.344 6804 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.344

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