[English] 日本語
Yorodumi
- PDB-4j70: Yeast 20S proteasome in complex with the belactosin derivative 3e -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 1336 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more