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- PDB-9aw7: Yeast 20S proteasome soaked with isolated TMC-95B -

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Basic information

Entry
Database: PDB / ID: 9aw7
TitleYeast 20S proteasome soaked with isolated TMC-95B
Components
  • (Proteasome subunit ...) x 4
  • (proteasome endopeptidase ...) x 2
  • PRE10 isoform 1
  • PRE5 isoform 1
  • PRE6 isoform 1
  • PRE7 isoform 1
  • PRE8 isoform 1
  • PRE9 isoform 1
  • PUP2 isoform 1
  • PUP3 isoform 1
KeywordsHYDROLASE
Function / homology
Function and homology information


proteasome core complex / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / 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 ...proteasome core complex / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / 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 / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome complex / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
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 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 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
Similarity search - Domain/homology
: / ACETIC ACID / PRE5 isoform 1 / PRE9 isoform 1 / PUP2 isoform 1 / PRE7 isoform 1 / Proteasome subunit beta / PRE6 isoform 1 / proteasome endopeptidase complex / PRE10 isoform 1 ...: / ACETIC ACID / PRE5 isoform 1 / PRE9 isoform 1 / PUP2 isoform 1 / PRE7 isoform 1 / Proteasome subunit beta / PRE6 isoform 1 / proteasome endopeptidase complex / PRE10 isoform 1 / proteasome endopeptidase complex / PUP3 isoform 1 / PRE8 isoform 1 / Proteasome subunit beta / Proteasome subunit alpha type-1 / Proteasome subunit beta type-1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsMeneghello, R. / Rustiguel, J.K. / Fernandes, A.Z.N. / Trivella, D.B.B.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Other private1709-19681 Brazil
Sao Paulo Research Foundation (FAPESP)2014/10753-9 Brazil
Sao Paulo Research Foundation (FAPESP)2019/17721-9 Brazil
CitationJournal: To be published
Title: High-throughput protein crystallography to empower natural product-based drug discovery
Authors: Meneghello, R. / Rustiguel, J.K. / Araujo, E.A. / Felicio, R. / Fernandes, A.Z.N. / Ferreira, E.L.F. / Gubiani, J.R. / Takeda, A.A.S. / Souza, A.A. / Silva, C.C.L. / Bertonha, A.F. / ...Authors: Meneghello, R. / Rustiguel, J.K. / Araujo, E.A. / Felicio, R. / Fernandes, A.Z.N. / Ferreira, E.L.F. / Gubiani, J.R. / Takeda, A.A.S. / Souza, A.A. / Silva, C.C.L. / Bertonha, A.F. / Trindade, D.M. / Cunha, T.M. / Cardoso, A.C. / Dessen, A. / Berlinck, R.G.S. / Nascimento, Z.F.Z. / Trivella, D.B.B.
History
DepositionMar 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PRE8 isoform 1
B: PRE9 isoform 1
C: PRE6 isoform 1
D: PUP2 isoform 1
E: PRE5 isoform 1
F: PRE10 isoform 1
G: Proteasome subunit alpha type-1
O: PRE8 isoform 1
P: PRE9 isoform 1
Q: PRE6 isoform 1
R: PUP2 isoform 1
S: PRE5 isoform 1
T: PRE10 isoform 1
U: Proteasome subunit alpha type-1
H: proteasome endopeptidase complex
I: PUP3 isoform 1
J: Proteasome subunit beta
K: proteasome endopeptidase complex
L: PRE7 isoform 1
M: Proteasome subunit beta
N: Proteasome subunit beta type-1
V: proteasome endopeptidase complex
W: PUP3 isoform 1
X: Proteasome subunit beta
Y: proteasome endopeptidase complex
Z: PRE7 isoform 1
a: Proteasome subunit beta
b: Proteasome subunit beta type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)741,029133
Polymers728,31028
Non-polymers12,719105
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.620, 299.912, 144.663
Angle α, β, γ (deg.)90.000, 112.597, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 8 types, 16 molecules AOBPCQDRESFTIWLZ

#1: Protein PRE8 isoform 1


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L1BIF8
#2: Protein PRE9 isoform 1


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PXC6
#3: Protein PRE6 isoform 1


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q273
#4: Protein PUP2 isoform 1


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PXN2
#5: Protein PRE5 isoform 1


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PTH4
#6: Protein PRE10 isoform 1


Mass: 31443.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q4M4
#9: Protein PUP3 isoform 1


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6L0YA22
#12: Protein PRE7 isoform 1


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0P3

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Proteasome subunit ... , 4 types, 8 molecules GUJXMaNb

#7: Protein Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28049.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21243
#10: Protein Proteasome subunit beta


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q0W2
#13: Protein Proteasome subunit beta


Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H8ULD3
#14: Protein Proteasome subunit beta type-1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component 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)
References: UniProt: P38624, proteasome endopeptidase complex

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Proteasome endopeptidase ... , 2 types, 4 molecules HVKY

#8: Protein proteasome endopeptidase complex


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q449, proteasome endopeptidase complex
#11: Protein proteasome endopeptidase complex


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: A0A6A5Q5W3, proteasome endopeptidase complex

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Non-polymers , 6 types, 357 molecules

#15: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 85 / Source method: obtained synthetically / Formula: SO4
#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Mg
#17: Chemical
ChemComp-A1AHA / TMC-95B


Mass: 680.705 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H40N6O10 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#19: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsKNOWN AS PROTEASOME INHIBITOR, TMC-95A INHIBITED THE CHYMOTRYPSIN-LIKE (CHT-L), TRYPSIN-LIKE (T-L), ...KNOWN AS PROTEASOME INHIBITOR, TMC-95A INHIBITED THE CHYMOTRYPSIN-LIKE (CHT-L), TRYPSIN-LIKE (T-L), AND PEPTIDYLGLUTAMYL-PEPTIDE HYDROLYZING (PGPH) ACTIVITIES OF 20S PROTEASOME
Has ligand of interestY
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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: MES 100 mM pH 5.5-6.9, MPD 8-18% and magnesium acetate 20 mM
PH range: 5.5-6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.91→30.04 Å / Num. obs: 228968 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 47.38 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.267 / Rpim(I) all: 0.109 / Rrim(I) all: 0.289 / Χ2: 1.02 / Net I/σ(I): 7.4 / Num. measured all: 1591363
Reflection shellResolution: 2.91→2.96 Å / % possible obs: 98.5 % / Redundancy: 7 % / Rmerge(I) obs: 1.526 / Num. measured all: 79070 / Num. unique obs: 11282 / CC1/2: 0.689 / Rpim(I) all: 0.617 / Rrim(I) all: 1.647 / Χ2: 1.02 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→30.04 Å / SU ML: 0.3896 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8474
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 11262 4.92 %
Rwork0.1944 217487 -
obs0.1962 228749 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.82 Å2
Refinement stepCycle: LAST / Resolution: 2.91→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49219 0 743 252 50214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002550971
X-RAY DIFFRACTIONf_angle_d0.549269090
X-RAY DIFFRACTIONf_chiral_restr0.04447724
X-RAY DIFFRACTIONf_plane_restr0.00428848
X-RAY DIFFRACTIONf_dihedral_angle_d12.79318725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-2.940.39593920.32937162X-RAY DIFFRACTION98.36
2.94-2.980.36373860.31727174X-RAY DIFFRACTION98.48
2.98-3.010.35083950.30387141X-RAY DIFFRACTION98.54
3.01-3.050.34393770.29487195X-RAY DIFFRACTION98.58
3.05-3.090.34493670.28657151X-RAY DIFFRACTION98.64
3.09-3.130.3323930.28427244X-RAY DIFFRACTION98.75
3.13-3.180.31673960.28067118X-RAY DIFFRACTION98.66
3.18-3.230.31953830.27327258X-RAY DIFFRACTION98.76
3.23-3.280.29933440.2597258X-RAY DIFFRACTION98.98
3.28-3.330.29383830.24717138X-RAY DIFFRACTION98.84
3.33-3.390.30783830.24237259X-RAY DIFFRACTION99.11
3.39-3.450.26553600.22227260X-RAY DIFFRACTION99
3.45-3.520.25313760.21277190X-RAY DIFFRACTION99.14
3.52-3.590.2664050.21177190X-RAY DIFFRACTION99.15
3.59-3.670.26474040.20857233X-RAY DIFFRACTION99.23
3.67-3.750.2423470.19857259X-RAY DIFFRACTION99.3
3.75-3.840.22344020.19697249X-RAY DIFFRACTION99.34
3.84-3.950.21023640.18517288X-RAY DIFFRACTION99.42
3.95-4.060.20863750.18017264X-RAY DIFFRACTION99.58
4.06-4.190.21663860.17077255X-RAY DIFFRACTION99.57
4.19-4.340.19033510.16217314X-RAY DIFFRACTION99.53
4.34-4.520.18863500.15197332X-RAY DIFFRACTION99.68
4.52-4.720.17813730.14297242X-RAY DIFFRACTION99.66
4.72-4.970.17433790.14457358X-RAY DIFFRACTION99.77
4.97-5.280.1813980.15667240X-RAY DIFFRACTION99.82
5.28-5.680.20353680.17587311X-RAY DIFFRACTION99.92
5.69-6.250.22113600.18297351X-RAY DIFFRACTION99.92
6.25-7.150.21723810.17267344X-RAY DIFFRACTION99.94
7.15-8.960.15113380.13157393X-RAY DIFFRACTION99.86
8.96-30.040.13843460.13927316X-RAY DIFFRACTION98.52

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