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- PDB-1iru: Crystal Structure of the mammalian 20S proteasome at 2.75 A resolution -

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Basic information

Entry
Database: PDB / ID: 1iru
TitleCrystal Structure of the mammalian 20S proteasome at 2.75 A resolution
Components(20S proteasome) x 14
KeywordsHYDROLASE / 20S proteasome / cell cycle / Immune response / proteolysis / ubiquitin
Function / homology
Function and homology information


Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN ...Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / G2/M Checkpoints / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX3 expression and activity / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / NIK-->noncanonical NF-kB signaling / Orc1 removal from chromatin / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Interleukin-1 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of beta-catenin by the destruction complex / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / UCH proteinases / Ub-specific processing proteases / Downstream TCR signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / The role of GTSE1 in G2/M progression after G2 checkpoint / ABC-family proteins mediated transport / Separation of Sister Chromatids / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / Neutrophil degranulation / proteasome core complex / immune system process / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteolysis involved in protein catabolic process / P-body / response to oxidative stress / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ciliary basal body / centrosome / mitochondrion / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Proteasome subunit alpha 1 / 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 subunit alpha 1 / 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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Proteasome subunit beta type-3 / Proteasome subunit beta type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-6 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-7 ...Proteasome subunit beta type-3 / Proteasome subunit beta type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-6 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-7 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsUnno, M. / Mizushima, T. / Morimoto, Y. / Tomisugi, Y. / Tanaka, K. / Yasuoka, N. / Tsukihara, T.
CitationJournal: Structure / Year: 2002
Title: The structure of the mammalian 20S proteasome at 2.75 A resolution.
Authors: Unno, M. / Mizushima, T. / Morimoto, Y. / Tomisugi, Y. / Tanaka, K. / Yasuoka, N. / Tsukihara, T.
History
DepositionOct 24, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 20S proteasome
B: 20S proteasome
C: 20S proteasome
D: 20S proteasome
E: 20S proteasome
F: 20S proteasome
G: 20S proteasome
H: 20S proteasome
I: 20S proteasome
J: 20S proteasome
K: 20S proteasome
L: 20S proteasome
M: 20S proteasome
N: 20S proteasome
O: 20S proteasome
P: 20S proteasome
Q: 20S proteasome
R: 20S proteasome
S: 20S proteasome
T: 20S proteasome
U: 20S proteasome
V: 20S proteasome
W: 20S proteasome
X: 20S proteasome
Y: 20S proteasome
Z: 20S proteasome
1: 20S proteasome
2: 20S proteasome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)718,07058
Polymers717,34128
Non-polymers72930
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)316.7, 205.9, 116.0
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Details28mer

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Components

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Protein , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZM1N2

#1: Protein 20S proteasome


Mass: 27432.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q2YDE4*PLUS
#2: Protein 20S proteasome


Mass: 25796.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q3T0Y5*PLUS
#3: Protein 20S proteasome


Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q3ZCK9*PLUS
#4: Protein 20S proteasome


Mass: 27929.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q3ZBG0*PLUS
#5: Protein 20S proteasome


Mass: 26494.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q5E987*PLUS
#6: Protein 20S proteasome


Mass: 29595.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q3T0X5*PLUS
#7: Protein 20S proteasome


Mass: 28338.057 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q58DU5*PLUS
#8: Protein 20S proteasome


Mass: 21921.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q3MHN0*PLUS
#9: Protein 20S proteasome


Mass: 25351.047 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q2TBP0*PLUS
#10: Protein 20S proteasome


Mass: 22954.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: P33672
#11: Protein 20S proteasome


Mass: 22864.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q5E9K0*PLUS
#12: Protein 20S proteasome


Mass: 22484.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q32KL2*PLUS
#13: Protein 20S proteasome


Mass: 23578.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q2TBX6*PLUS
#14: Protein 20S proteasome


Mass: 24402.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: liver / References: UniProt: Q3T108*PLUS

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Non-polymers , 2 types, 195 molecules

#15: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Mg
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, Mg acetate, Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 25 ℃ / Details: Tomisugi, Y., (2000) J. Biochem., 127, 941.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.15 Mmagnesium acetate1reservoir
20.1 Msodium cacodylate1reservoirpH6.5
335 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: the rotated-inclined double-crystal monochrometer
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→72.55 Å / Num. all: 189429 / Num. obs: 189429 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.75→2.82 Å / % possible all: 70
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 733250 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 70 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
CNSrefinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→65 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 9420 4.98 %RANDOM
Rwork0.25 ---
all0.252 189241 --
obs0.252 189241 --
Refinement stepCycle: LAST / Resolution: 2.75→65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47562 0 30 165 47757
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.40445
X-RAY DIFFRACTIONc_bond_d0.007686
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.25 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4

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