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- PDB-1ryp: CRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST AT 2.4 ANGSTRO... -

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Basic information

Entry
Database: PDB / ID: 1ryp
TitleCRYSTAL STRUCTURE OF THE 20S PROTEASOME FROM YEAST AT 2.4 ANGSTROMS RESOLUTION
Components(20S PROTEASOME) x 14
KeywordsMULTICATALYTIC PROTEINASE / 20S PROTEASOME / PROTEIN DEGRADATION / ANTIGEN PROCESSING / HYDROLASE / PROTEASE
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol
Similarity search - Function
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. ...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
Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 ...Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsGroll, M. / Ditzel, L. / Loewe, J. / Stock, D. / Bochtler, M. / Bartunik, H.D. / Huber, R.
CitationJournal: Nature / Year: 1997
Title: Structure of 20S proteasome from yeast at 2.4 A resolution.
Authors: Groll, M. / Ditzel, L. / Lowe, J. / Stock, D. / Bochtler, M. / Bartunik, H.D. / Huber, R.
History
DepositionFeb 26, 1997Processing site: BNL
Revision 1.0Apr 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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 / _software.name / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)706,51748
Polymers706,03028
Non-polymers48620
Water52,3882908
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120760 Å2
ΔGint-524 kcal/mol
Surface area216760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.490, 300.700, 144.420
Angle α, β, γ (deg.)90.00, 112.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZM1N2

#1: Protein 20S PROTEASOME


Mass: 27316.037 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21243, EC: 3.4.99.46
#2: Protein 20S PROTEASOME


Mass: 27191.828 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23639, EC: 3.4.99.46
#3: Protein 20S PROTEASOME


Mass: 27050.416 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23638, EC: 3.4.99.46
#4: Protein 20S PROTEASOME


Mass: 26903.330 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40303, EC: 3.4.99.46
#5: Protein 20S PROTEASOME


Mass: 26544.789 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32379, EC: 3.4.99.46
#6: Protein 20S PROTEASOME


Mass: 25502.805 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40302, EC: 3.4.99.46
#7: Protein 20S PROTEASOME


Mass: 26892.482 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21242, EC: 3.4.99.46
#8: Protein 20S PROTEASOME


Mass: 22401.266 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38624, EC: 3.4.99.46
#9: Protein 20S PROTEASOME


Mass: 23987.254 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25043, EC: 3.4.99.46
#10: Protein 20S PROTEASOME


Mass: 22496.645 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25451, EC: 3.4.99.46
#11: Protein 20S PROTEASOME


Mass: 22545.676 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22141, EC: 3.4.99.46
#12: Protein 20S PROTEASOME


Mass: 23353.262 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30656, EC: 3.4.99.46
#13: Protein 20S PROTEASOME


Mass: 24883.928 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23724, EC: 3.4.99.46
#14: Protein 20S PROTEASOME


Mass: 25945.496 Da / Num. of mol.: 2 / Mutation: CHAINS H, V, T1A, CHAIN L, Z, K33R / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30657, EC: 3.4.99.46

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Non-polymers , 2 types, 2928 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2908 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growpH: 6.9 / Details: pH 6.9
Crystal grow
*PLUS
Temperature: 24 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127 mg/mlprotein1drop
26.7 mMTris-HCl1drop
30.7 mMEDTA1drop
413 mMmagnesium acetate1drop
50.03 Mmorpholino ethane sulphonic acid1drop
64 %2,4-methylpentanediol1drop
740 mMmagnesium acetate1reservoir
80.1 Mmorpholino ethane sulphonic acid1reservoir
912 %2,4-methylpentanediol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 778118 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 2
Reflection shellHighest resolution: 1.97 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2 / % possible all: 93.6

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMV. 5.3data reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementStarting model: PDB ENTRY 1PMA

1pma


Resolution: 1.9→50 Å / Rfactor Rfree error: 0 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.33 37408 5 %
Rwork0.286 --
obs0.286 752101 90.5 %
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.4 Å20 Å24.5 Å2
2--13.9 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49676 0 20 2928 52624
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.21.5
X-RAY DIFFRACTIONx_mcangle_it4.62
X-RAY DIFFRACTIONx_scbond_it4.62
X-RAY DIFFRACTIONx_scangle_it6.72.5
Refine LS restraints NCSRms dev Biso : 2 Å2 / Rms dev position: 0.15 Å / Weight Biso : 2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.33
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34

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