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- PDB-1jd2: Crystal Structure of the yeast 20S Proteasome:TMC-95A complex: A ... -

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Basic information

Entry
Database: PDB / ID: 1jd2
TitleCrystal Structure of the yeast 20S Proteasome:TMC-95A complex: A non-covalent Proteasome Inhibitor
Components
  • (PROTEASOME COMPONENT ...) x 14
  • TMC-95A inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / beta-sandwich / proteasome:inhibitor complex / 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 / 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 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 / 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 / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / Ub-specific processing proteases / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / peroxisome / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / 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 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
TMC-95A / 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 ...TMC-95A / 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)
Apiospora montagnei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsGroll, M. / Koguchi, Y. / Huber, R. / Kohno, J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of the 20 S proteasome:TMC-95A complex: a non-covalent proteasome inhibitor.
Authors: Groll, M. / Koguchi, Y. / Huber, R. / Kohno, J.
History
DepositionJun 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software

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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 PUP1
P: PROTEASOME COMPONENT PUP3
Q: PROTEASOME COMPONENT C11
R: PROTEASOME COMPONENT PRE2
S: PROTEASOME COMPONENT C5
T: PROTEASOME COMPONENT PRE4
U: PROTEASOME COMPONENT PRE3
V: PROTEASOME COMPONENT Y7
W: PROTEASOME COMPONENT Y13
X: PROTEASOME COMPONENT PRE6
Y: PROTEASOME COMPONENT PUP2
Z: PROTEASOME COMPONENT PRE5
1: PROTEASOME COMPONENT C1
2: PROTEASOME COMPONENT C7-ALPHA
8: TMC-95A inhibitor
9: TMC-95A inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)705,81140
Polymers705,56830
Non-polymers24310
Water52,1172893
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area122240 Å2
ΔGint-479 kcal/mol
Surface area223180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.200, 301.300, 144.800
Angle α, β, γ (deg.)90.00, 112.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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PROTEASOME COMPONENT ... , 14 types, 28 molecules AVBWCXDYEZF1G2HOIPJQKRLSMTNU

#1: Protein PROTEASOME COMPONENT Y7 / E.C.3.4.99.46 / MACROPAIN SUBUNIT Y7 / PROTEINASE YSCE SUBUNIT 7 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT Y7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P23639, EC: 3.4.99.46
#2: Protein PROTEASOME COMPONENT Y13 / E.C.3.4.99.46 / MACROPAIN SUBUNIT Y13 / PROTEINASE YSCE SUBUNIT 13 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT Y13


Mass: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P23638, EC: 3.4.99.46
#3: Protein PROTEASOME COMPONENT PRE6 / E.C.3.4.99.46 / MACROPAIN SUBUNIT PRE6 / PROTEINASE YSCE SUBUNIT PRE6 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE6


Mass: 26903.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P40303, EC: 3.4.99.46
#4: Protein PROTEASOME COMPONENT PUP2 / E.C.3.4.99.46 / MACROPAIN SUBUNIT PUP2 / PROTEINASE YSCE SUBUNIT PUP2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP2


Mass: 26544.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P32379, EC: 3.4.99.46
#5: Protein PROTEASOME COMPONENT PRE5 / E.C.3.4.99.46 / MACROPAIN SUBUNIT PRE5 / PROTEINASE YSCE SUBUNIT PRE5 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE5


Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P40302, EC: 3.4.99.46
#6: Protein PROTEASOME COMPONENT C1 / E.C.3.4.99.46 / MACROPAIN SUBUNIT C1 / PROTEINASE YSCE SUBUNIT 1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C1


Mass: 26892.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P21242, EC: 3.4.99.46
#7: Protein PROTEASOME COMPONENT C7-ALPHA / E.C.3.4.99.46 / MACROPAIN SUBUNIT C7-ALPHA / PROTEINASE YSCE SUBUNIT 7 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX C7 / ...MACROPAIN SUBUNIT C7-ALPHA / PROTEINASE YSCE SUBUNIT 7 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX C7 / COMPONENT Y8 / SCL1 SUPPRESSOR PROTEIN


Mass: 27316.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P21243, EC: 3.4.99.46
#8: Protein PROTEASOME COMPONENT PUP1 / E.C.3.4.99.46 / MACROPAIN SUBUNIT PUP1 / PROTEINASE YSCE SUBUNIT PUP1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP1


Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P25043, EC: 3.4.99.46
#9: Protein PROTEASOME COMPONENT PUP3 / E.C.3.4.99.46 / MACROPAIN SUBUNIT PUP3 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP3


Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P25451, EC: 3.4.99.46
#10: Protein PROTEASOME COMPONENT C11 / E.C.3.4.99.46 / MACROPAIN SUBUNIT C11 / PROTEINASE YSCE SUBUNIT 11 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P22141, EC: 3.4.99.46
#11: Protein PROTEASOME COMPONENT PRE2 / E.C.3.4.99.46 / MACROPAIN SUBUNIT PRE2 / PROTEINASE YSCE SUBUNIT PRE2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE2


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P30656, EC: 3.4.99.46
#12: Protein PROTEASOME COMPONENT C5 / E.C.3.4.99.46 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P23724, EC: 3.4.99.46
#13: Protein PROTEASOME COMPONENT PRE4 / E.C.3.4.99.46 / MACROPAIN SUBUNIT PRE4 / PROTEINASE YSCE SUBUNIT PRE4 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE4


Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P30657, EC: 3.4.99.46
#14: Protein PROTEASOME COMPONENT PRE3 / E.C.3.4.99.46 / MACROPAIN SUBUNIT PRE3 / PROTEINASE YSCE SUBUNIT PRE3 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: part of 20S subunit / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: Sub61 / References: UniProt: P38624, EC: 3.4.99.46

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Protein/peptide , 1 types, 2 molecules 89

#15: Protein/peptide TMC-95A inhibitor


Type: Cyclic peptide / Class: Inhibitor / Mass: 680.705 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Apiospora montagnei (fungus) / References: TMC-95A

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Non-polymers , 2 types, 2903 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


Mass: 18.015 Da / Num. of mol.: 2893 / 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

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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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: MPD, MES, DMSO, magnesium Acetate, pH 6.4, VAPOR DIFFUSION, HANGING DROP at 293K
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 mMMES1reservoirpH7.2
610 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 12, 2001 / Details: high intensity beamline
RadiationMonochromator: SILICIUM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 742209 / Num. obs: 741075 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 69.354 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 4.22
Reflection
*PLUS
Num. obs: 255383 / Num. measured all: 741075

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Processing

Software
NameVersionClassification
MAR345data collection
TRUNCATEdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4(TRUNCATE)data scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3→50 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.336 37054 5 %random
Rwork0.251 ---
all0.274 742209 --
obs0.271 741075 --
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49646 0 10 2893 52549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.987
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.336 / Rfactor Rwork: 0.271

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