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- PDB-4j70: Yeast 20S proteasome in complex with the belactosin derivative 3e -

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Basic information

Entry
Database: PDB / ID: 4j70
TitleYeast 20S proteasome in complex with the belactosin derivative 3e
Components(Proteasome component ...) x 14
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Proteasome / drug discovery / irreversible inhibition / beta-lactone / Ntn hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
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 / proteasome endopeptidase complex / endopeptidase activator activity / proteasome core complex, beta-subunit complex / Ub-specific processing proteases / 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
BENZYL [(2S)-1-({(2R)-1-[(1S,2S)-2-{[(2R,3S,4S)-3-FORMYL-2-HYDROXY-4-METHYLHEXANOYL]AMINO}CYCLOPROPYL]-4-PHENYLBUTAN-2-YL}AMINO)-1-OXOPROPAN-2-YL]CARBAMATE / Chem-1KR / 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 ...BENZYL [(2S)-1-({(2R)-1-[(1S,2S)-2-{[(2R,3S,4S)-3-FORMYL-2-HYDROXY-4-METHYLHEXANOYL]AMINO}CYCLOPROPYL]-4-PHENYLBUTAN-2-YL}AMINO)-1-OXOPROPAN-2-YL]CARBAMATE / Chem-1KR / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKawamura, S. / Unno, Y. / List, A. / Tanaka, M. / Sasaki, T. / Arisawa, M. / Asai, A. / Groll, M. / Shuto, S.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Potent Proteasome Inhibitors Derived from the Unnatural cis-Cyclopropane Isomer of Belactosin A: Synthesis, Biological Activity, and Mode of Action.
Authors: Kawamura, S. / Unno, Y. / List, A. / Mizuno, A. / Tanaka, M. / Sasaki, T. / Arisawa, M. / Asai, A. / Groll, M. / Shuto, S.
History
DepositionFeb 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Sep 20, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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: 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
a: Proteasome component PRE4
b: Proteasome component PRE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)729,67130
Polymers728,54028
Non-polymers1,1312
Water24,0681336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area117980 Å2
ΔGint-341 kcal/mol
Surface area218170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.080, 301.710, 146.230
Angle α, β, γ (deg.)90.00, 113.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999907, 0.000346, 0.013605), (-0.002602, -0.986107, -0.166092), (0.013358, -0.166112, 0.986016)68.51759, -290.68921, -24.58945

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Components

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

#1: Protein Proteasome component Y7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein Proteasome component Y13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein Proteasome component PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome component PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein Proteasome component PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P40302, proteasome endopeptidase complex
#6: Protein Proteasome component C1


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P21242, proteasome endopeptidase complex
#7: Protein Proteasome component C7-alpha


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P21243, proteasome endopeptidase complex
#8: Protein Proteasome component PUP1


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome component PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome component C11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome component PRE2


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


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome component PRE4


Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome component PRE3


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

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Non-polymers , 2 types, 1338 molecules

#15: Chemical ChemComp-1KR / benzyl [(2S)-1-({(2R)-1-[(1S,2S)-2-{[(2R,3S,4S)-3-formyl-2-hydroxy-4-methylhexanoyl]amino}cyclopropyl]-4-phenylbutan-2-yl}amino)-1-oxopropan-2-yl]carbamate


Type: Peptide-like / Class: Inhibitor / Mass: 565.700 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H43N3O6
References: BENZYL [(2S)-1-({(2R)-1-[(1S,2S)-2-{[(2R,3S,4S)-3-FORMYL-2-HYDROXY-4-METHYLHEXANOYL]AMINO}CYCLOPROPYL]-4-PHENYLBUTAN-2-YL}AMINO)-1-OXOPROPAN-2-YL]CARBAMATE
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1336 / 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: 3.8 Å3/Da / Density % sol: 67.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 20 mM magnesium acetate, 0.1 M MES, 12% MPD, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2011
RadiationMonochromator: LN2-cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 266454 / Num. obs: 262724 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 10
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.474 / % possible all: 92

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RYP

1ryp


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.723 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.521 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22379 13137 5 %RANDOM
Rwork0.17237 ---
obs0.17491 249586 98.92 %-
all-249586 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.473 Å2
Baniso -1Baniso -2Baniso -3
1-4.08 Å2-0 Å2-0.67 Å2
2---7.35 Å2-0 Å2
3---2.58 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49538 0 82 1336 50956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01950538
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.96568368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50756338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17524.4082264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.023158778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.29615288
X-RAY DIFFRACTIONr_chiral_restr0.1040.27704
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02137994
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1585TIGHT POSITIONAL0.050.05
1A1637TIGHT POSITIONAL0.050.05
1A1757TIGHT POSITIONAL0.050.05
1A1824TIGHT POSITIONAL0.050.05
1A1512TIGHT POSITIONAL0.050.05
1A1915TIGHT THERMAL5.670.5
2B1905TIGHT THERMAL4.810.5
3C1891TIGHT THERMAL6.870.5
4D1862TIGHT THERMAL4.530.5
5E1795TIGHT THERMAL4.520.5
6F1897TIGHT THERMAL4.790.5
7G1921TIGHT THERMAL4.260.5
8H1685TIGHT THERMAL3.670.5
9I1581TIGHT THERMAL3.040.5
10J1585TIGHT THERMAL3.50.5
11K1637TIGHT THERMAL30.5
12L1757TIGHT THERMAL3.060.5
13M1824TIGHT THERMAL3.040.5
14N1512TIGHT THERMAL3.040.5
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 864 -
Rwork0.305 16399 -
obs--91.22 %

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