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Basic information

Entry
Database: PDB / ID: 1g65
TitleCrystal structure of epoxomicin:20s proteasome reveals a molecular basis for selectivity of alpha,beta-epoxyketone proteasome inhibitors
Components
  • (Proteasome component ...) x 14
  • EPOXOMICIN (peptide inhibitor)
KeywordsHYDROLASE/HYDROLASE inhibitor / proteasome / epoxomicin / ubiquitin / ntn-hydolase / protease / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm
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 alpha6 / Proteasome subunit alpha5 / 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 alpha6 / Proteasome subunit alpha5 / 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 / 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)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGroll, M. / Kim, K.B. / Kairies, N. / Huber, R. / Crews, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2000
Title: Crystal Structure of Epoxomicin:20S Proteasome reveals a molecular basis for selectivity of alpha,beta-Epoxyketone Proteasome Inhibitors
Authors: Groll, M. / Kim, K.B. / Kairies, N. / Crews, C.
History
DepositionNov 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome component Y7
B: Proteasome component Y13
C: Proteasome component PRE6
D: Proteasome component PUP2
E: Proteasome component PRE5
F: Proteasome component C1
G: Proteasome component C7-alpha
H: Proteasome component PUP1
I: Proteasome component PUP3
J: Proteasome component C11
K: Proteasome component PRE2
L: Proteasome component C5
M: Proteasome component PRE4
N: Proteasome component PRE3
O: Proteasome component Y7
P: Proteasome component Y13
Q: Proteasome component PRE6
R: Proteasome component PUP2
S: Proteasome component PRE5
T: Proteasome component C1
U: Proteasome component C7-alpha
V: Proteasome component PUP1
W: Proteasome component PUP3
X: Proteasome component C11
Y: Proteasome component PRE2
Z: Proteasome component C5
1: Proteasome component PRE4
2: Proteasome component PRE3
3: EPOXOMICIN (peptide inhibitor)
4: EPOXOMICIN (peptide inhibitor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)705,53540
Polymers705,29230
Non-polymers24310
Water51,7392872
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120880 Å2
ΔGint-431 kcal/mol
Surface area216490 Å2
Unit cell
Length a, b, c (Å)135.2, 300.2, 144.02
Angle α, β, γ (deg.)90, 112.98, 90
Int Tables number4
Space group name H-MP1211
Detailsone 20S proteasome per asymmetric unit

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Components

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Proteasome component ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZM1N2

#1: Protein Proteasome component Y7 / / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein Proteasome component Y13 / / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteinase YSCE subunit 13


Mass: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein Proteasome component PRE6 / / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteinase YSCE subunit PRE6


Mass: 26903.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome component PUP2 / / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteinase YSCE subunit PUP2


Mass: 26544.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein Proteasome component PRE5 / / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteinase YSCE subunit PRE5


Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P40302, proteasome endopeptidase complex
#6: Protein Proteasome component C1 / / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteinase YSCE subunit 1


Mass: 26892.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P21242, proteasome endopeptidase complex
#7: Protein Proteasome component C7-alpha / / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component Y8 / ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 27316.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P21243, proteasome endopeptidase complex
#8: Protein Proteasome component PUP1 / / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteinase YSCE subunit PUP1


Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome component PUP3 / / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3


Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome component C11 / / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome component PRE2 / / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteinase YSCE subunit PRE2


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome component C5 / / Multicatalytic endopeptidase complex subunit C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome component PRE4 / / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteinase YSCE subunit PRE4


Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome component PRE3 / / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteinase YSCE subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / Strain: SC288
References: UniProt: P38624, proteasome endopeptidase complex

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Protein/peptide , 1 types, 2 molecules 34

#15: Protein/peptide EPOXOMICIN (peptide inhibitor)


Mass: 542.752 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The natural product epoxomicin was isolated from an Actinomycetes strain

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Non-polymers , 2 types, 2882 molecules

#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#17: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2872 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE STARTING EPOXIDE RING OF EPOXOMICIN (CHAINS 3 AND 4) UNDERGOES RE-CYCLIZATION REACTION WITH THE ...THE STARTING EPOXIDE RING OF EPOXOMICIN (CHAINS 3 AND 4) UNDERGOES RE-CYCLIZATION REACTION WITH THE SIDE CHAIN OF N-TERMINAL THR RESIDUE OF CHAINS K AND Y, RESPECTIVELY. SEE ALSO LINK RECORDS

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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: 3.82 Å3/Da / Density % sol: 67.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1M Mes, pH 6.8 11% MPD 25mM MgAc2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
31 mMEDTA1drop
430 mMmagnesium acetate1reservoir
5100 mMMES1reservoirpH6.9
611 %MPD1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 19, 1999
RadiationMonochromator: Silicium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. all: 1336712 / Num. obs: 427960 / % possible obs: 91.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 8.3
Reflection shellResolution: 2.25→2.34 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.395 / % possible all: 91.1
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 1336712
Reflection shell
*PLUS
Lowest resolution: 2.35 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wt yeast 20S proteasome (1RYP)

1ryp


Resolution: 2.25→20 Å / σ(F): 3 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.336 21398 Random
Rwork0.283 --
obs0.286 427960 -
all-1336712 -
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49626 0 10 2872 52508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONrms-bond0.012
X-RAY DIFFRACTIONrms-angles1.946
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 3 / Rfactor obs: 0.283
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_d1.946

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