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- PDB-3bdm: yeast 20S proteasome:glidobactin A-complex -

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Basic information

Entry
Database: PDB / ID: 3bdm
Titleyeast 20S proteasome:glidobactin A-complex
Components(Proteasome component ...) x 14
KeywordsHYDROLASE / proteasome / ubiquitin / proteolysis / pathogen / virulence factor / Cytoplasm / Nucleus / Protease / Threonine protease / Ubl conjugation / Phosphoprotein / Zymogen
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
Chem-GDT / 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 ...Chem-GDT / 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: 2.7 Å
AuthorsGroll, M. / Dudler, R. / Kaiser, M.
CitationJournal: Nature / Year: 2008
Title: A plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism
Authors: Groll, M. / Schellenberg, B. / Bachmann, A.S. / Archer, C.R. / Huber, R. / Powell, T.K. / Lindow, S. / Kaiser, M. / Dudler, R.
History
DepositionNov 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
0: Proteasome component PRE4
1: Proteasome component PRE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)741,45432
Polymers739,37128
Non-polymers2,0834
Water24,0681336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area116940 Å2
ΔGint-351.6 kcal/mol
Surface area214340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.770, 302.790, 143.210
Angle α, β, γ (deg.)90.00, 112.24, 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 AOBPCQDRESFTGUHVIWJXKYLZM0N1

#1: Protein Proteasome component Y7 / 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 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein Proteasome component Y13 / Macropain subunit Y13 / Proteinase YSCE subunit 13 / Multicatalytic endopeptidase complex subunit Y13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein Proteasome component PRE6 / Macropain subunit PRE6 / Proteinase YSCE subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome component PUP2 / Macropain subunit PUP2 / Proteinase YSCE subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein Proteasome component PRE5 / Macropain subunit PRE5 / Proteinase YSCE subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P40302, proteasome endopeptidase complex
#6: Protein Proteasome component C1 / Macropain subunit C1 / Proteinase YSCE subunit 1 / Multicatalytic endopeptidase complex subunit C1


Mass: 31443.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P21242, proteasome endopeptidase complex
#7: Protein Proteasome component C7-alpha / Macropain subunit C7- alpha / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex C7 / ...Macropain subunit C7- alpha / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex C7 / Proteasome component Y8 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P21243, proteasome endopeptidase complex
#8: Protein Proteasome component PUP1 / Macropain subunit PUP1 / Proteinase YSCE subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome component PUP3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome component C11 / 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 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome component PRE2 / 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 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome component C5 / Multicatalytic endopeptidase complex subunit C5


Mass: 26905.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome component PRE4 / Macropain subunit PRE4 / Proteinase YSCE subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4


Mass: 29471.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome component PRE3 / 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 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: w303
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 2 types, 1340 molecules

#15: Chemical
ChemComp-GDT / (2E,4E)-N-[(2S,3R)-3-hydroxy-1-[[(3Z,5S,8S,10S)-10-hydroxy-5-methyl-2,7-dioxo-1,6-diazacyclododec-3-en-8-yl]amino]-1-ox obutan-2-yl]dodeca-2,4-dienamide / Glidobactin A


Mass: 520.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H44N4O6
#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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 100mM Mes, 14% MPD, 30mM MgAc2, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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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: Jun 30, 2007
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→99 Å / Num. all: 384026 / Num. obs: 368665 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 13.3
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3 / % possible all: 85.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Enty 1RYP

1ryp


Resolution: 2.7→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 6539959.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 13733 5 %RANDOM
Rwork0.234 ---
all0.236 368665 --
obs0.234 277188 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.0612 Å2 / ksol: 0.355456 e/Å3
Displacement parametersBiso mean: 55.6 Å2
Baniso -1Baniso -2Baniso -3
1-14.18 Å20 Å2-2.83 Å2
2---24.02 Å20 Å2
3---9.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.78 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49538 0 148 1336 51022
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.431 2058 4.9 %
Rwork0.423 39728 -
obs--88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4gld.param

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