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- PDB-3shj: Proteasome in complex with hydroxyurea derivative HU10 -

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Basic information

Entry
Database: PDB / ID: 3shj
TitleProteasome in complex with hydroxyurea derivative HU10
Components(Proteasome component ...) x 14
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ubiquitin / drug development / cancer / immunology / protein degradation / unfolded protein substrates / 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
Chem-H10 / 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-H10 / 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
AuthorsGallastegui, N. / Beck, P. / Arciniega, M. / Hillebrand, S. / Huber, R. / Groll, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: Hydroxyureas as noncovalent proteasome inhibitors.
Authors: Gallastegui, N. / Beck, P. / Arciniega, M. / Huber, R. / Hillebrand, S. / Groll, M.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_ins_code / _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
1: Proteasome component PRE4
2: Proteasome component PRE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)705,30632
Polymers704,20628
Non-polymers1,0994
Water23,0771281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area117600 Å2
ΔGint-333 kcal/mol
Surface area212240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.117, 300.565, 144.058
Angle α, β, γ (deg.)90.00, 112.76, 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 AOBPCQDRESFTGUHVIWJXKYLZM1N2

#1: Protein Proteasome component Y7 / / Proteasomal alpha 2 subunit / a2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex ...Proteasomal alpha 2 subunit / a2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein Proteasome component Y13 / / Proteasomal alpha 3 subunit / a3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex ...Proteasomal alpha 3 subunit / a3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteinase YSCE subunit 13


Mass: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein Proteasome component PRE6 / / Proteasomal alpha 4 subunit / a4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex ...Proteasomal alpha 4 subunit / a4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteinase YSCE subunit PRE6


Mass: 26903.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome component PUP2 / / Proteasomal alpha 5 subunit / a5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex ...Proteasomal alpha 5 subunit / a5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteinase YSCE subunit PUP2


Mass: 26544.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein Proteasome component PRE5 / / Proteasomal alpha 6 subunit / a6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex ...Proteasomal alpha 6 subunit / a6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteinase YSCE subunit PRE5


Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P40302, proteasome endopeptidase complex
#6: Protein Proteasome component C1 / / Proteasomal alpha 7 subunit / a7 / Macropain subunit C1 / Multicatalytic endopeptidase complex ...Proteasomal alpha 7 subunit / a7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteinase YSCE subunit 1


Mass: 26892.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21242, proteasome endopeptidase complex
#7: Protein Proteasome component C7-alpha / / Proteasomal alpha 1 subunit / a1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase ...Proteasomal alpha 1 subunit / a1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 27316.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21243, proteasome endopeptidase complex
#8: Protein Proteasome component PUP1 / / Proteasomal beta 2 subunit / b2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex ...Proteasomal beta 2 subunit / b2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteinase YSCE subunit PUP1


Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome component PUP3 / / Proteasomal beta 3 subunit / b3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3


Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome component C11 / / Proteasomal beta 4 subunit / b4 / Macropain subunit C11 / Multicatalytic endopeptidase complex ...Proteasomal beta 4 subunit / b4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome component PRE2 / / Proteasomal beta 5 subunit / b5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex ...Proteasomal beta 5 subunit / b5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteinase YSCE 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: ATCC 204508 / S288c
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome component C5 / / Proteasomal beta 6 subunit / b6 / Multicatalytic endopeptidase complex subunit C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome component PRE4 / / Proteasomal beta 7 subunit / b7 / Macropain subunit PRE4 / Multicatalytic endopeptidase complex ...Proteasomal beta 7 subunit / b7 / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteinase YSCE subunit PRE4


Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome component PRE3 / / Proteasomal beta 1 subunit / b1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex ...Proteasomal beta 1 subunit / b1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit 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) / Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex

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Non-polymers , 3 types, 1285 molecules

#15: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#16: Chemical ChemComp-H10 / 1-hydroxy-1-[(2R)-4-{3-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yloxy]phenyl}but-3-yn-2-yl]urea


Mass: 354.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H26N2O3
#17: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1281 / 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: 3.8 Å3/Da / Density % sol: 67.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM magnesium acetate, 11% PEG, 100 mM MES/NaOH, pH 7.0, crystals grow to their final size within a week, 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
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2010
RadiationMonochromator: Fixed-exit LN2-cooled Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.765 Å / Num. all: 257564 / Num. obs: 250186 / % possible obs: 91.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2 / % possible all: 90.2

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Processing

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

1ryp


Resolution: 2.8→49.765 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 6597707.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.266 11684 5 %RANDOM
Rwork0.238 ---
obs0.238 234733 92.3 %-
all-246417 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.418 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 65.9 Å2
Baniso -1Baniso -2Baniso -3
1-31.42 Å20 Å2-20.72 Å2
2---36.7 Å20 Å2
3---5.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a1.1 Å1.05 Å
Refinement stepCycle: LAST / Resolution: 2.8→49.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49548 0 76 1281 50905
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.76
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.489 1989 5.1 %
Rwork0.47 36949 -
obs--91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4combine.par

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