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- PDB-3d29: Proteasome Inhibition by Fellutamide B -

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Basic information

Entry
Database: PDB / ID: 3d29
TitleProteasome Inhibition by Fellutamide B
Components
  • (Proteasome subunit ...) x 3
  • (proteasome endopeptidase ...) x 2
  • Fellutamide B
  • PRE10 isoform 1
  • PRE5 isoform 1
  • PRE6 isoform 1
  • PRE7 isoform 1
  • PRE8 isoform 1
  • PRE9 isoform 1
  • PUP2 isoform 1
  • PUP3 isoform 1
  • SCL1 isoform 1
KeywordsHYDROLASE / anti-parallel beta-sheet structure flanked by alpha-helices / Cytoplasm / Nucleus / Protease / Proteasome / Threonine protease / Ubl conjugation / Phosphoprotein / Zymogen
Function / homology
Function and homology information


proteasome core complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / 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 ...proteasome core complex / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / 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 / endopeptidase activator activity / Ub-specific processing proteases / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / Neutrophil degranulation / proteasome complex / peroxisome / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(3R)-3-HYDROXYDODECANOIC ACID / PRE5 isoform 1 / PRE9 isoform 1 / PUP2 isoform 1 / SCL1 isoform 1 / PRE7 isoform 1 / Proteasome subunit beta / PRE6 isoform 1 / proteasome endopeptidase complex / PRE10 isoform 1 ...(3R)-3-HYDROXYDODECANOIC ACID / PRE5 isoform 1 / PRE9 isoform 1 / PUP2 isoform 1 / SCL1 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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsGroll, M. / Hines, J. / Fahnestock, M. / Crews, M.C.
CitationJournal: Chem.Biol. / Year: 2008
Title: Proteasome Inhibition by Fellutamide B Induces Nerve Growth Factor Synthesis
Authors: Hines, J. / Groll, M. / Fahnestock, M. / Crews, C.M.
History
DepositionMay 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Mar 27, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_rmsd_bond / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _cell.Z_PDB / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: SCL1 isoform 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
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: SCL1 isoform 1
V: proteasome endopeptidase complex
W: PUP3 isoform 1
X: Proteasome subunit beta
Y: proteasome endopeptidase complex
Z: PRE7 isoform 1
1: Proteasome subunit beta
2: Proteasome subunit beta type-1
a: Fellutamide B
b: Fellutamide B
c: Fellutamide B
d: Fellutamide B
e: Fellutamide B
f: Fellutamide B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)707,74540
Polymers706,44734
Non-polymers1,2986
Water23,9961332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.272, 301.580, 143.454
Angle α, β, γ (deg.)90.00, 112.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 9 types, 18 molecules AOBPCQDRESFTGUIWLZ

#1: Protein PRE8 isoform 1


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6L1BIF8, UniProt: P23639*PLUS
#2: Protein PRE9 isoform 1


Mass: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5PXC6, UniProt: P23638*PLUS
#3: Protein PRE6 isoform 1


Mass: 26903.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5Q273, UniProt: P40303*PLUS
#4: Protein PUP2 isoform 1


Mass: 26544.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5PXN2, UniProt: P32379*PLUS
#5: Protein PRE5 isoform 1


Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5PTH4, UniProt: P40302*PLUS
#6: Protein PRE10 isoform 1


Mass: 26892.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5Q4M4, UniProt: P21242*PLUS
#7: Protein SCL1 isoform 1


Mass: 27316.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5PYC9, UniProt: P21243*PLUS
#9: Protein PUP3 isoform 1


Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6L0YA22, UniProt: P25451*PLUS
#12: Protein PRE7 isoform 1


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5Q0P3, UniProt: P23724*PLUS

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

#8: Protein proteasome endopeptidase complex


Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast
References: UniProt: A0A6A5Q449, UniProt: P25043*PLUS, proteasome endopeptidase complex
#11: Protein proteasome endopeptidase complex


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast
References: UniProt: A0A6A5Q5W3, UniProt: P30656*PLUS, proteasome endopeptidase complex

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Proteasome subunit ... , 3 types, 6 molecules JXM1N2

#10: Protein Proteasome subunit beta


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A6A5Q0W2, UniProt: P22141*PLUS
#13: Protein Proteasome subunit beta


Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast / References: UniProt: A0A8H8ULD3, UniProt: P30657*PLUS
#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 / Details: native purification from cell lysate / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: bakers yeast
References: UniProt: P38624, proteasome endopeptidase complex

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Protein/peptide , 1 types, 6 molecules abcdef

#15: Protein/peptide
Fellutamide B


Mass: 373.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 1338 molecules

#16: Chemical
ChemComp-HXD / (3R)-3-HYDROXYDODECANOIC ACID / 3-OH-DODECANOATE


Mass: 216.317 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H24O3
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1332 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE ALDEHYDE OF FELLUTAMIDE B REACT WITH THR1 OGAMMA BY HEMIACETAL-FORMATION

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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: 67.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10 % MPD; 0,1 M MES, 30 mM MgAc2, pH 6,8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 6,8

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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: Apr 28, 2006 / Details: DYNAMICALLY BENDABLE MIRROR
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: 2.6→40 Å / Num. all: 331875 / Num. obs: 336246 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.6→2.63 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB Entry 1ryp

1ryp


Resolution: 2.6→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3868824.43 / 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
Rfree0.266 15649 5 %RANDOM
Rwork0.24 ---
all0.2413 318163 --
obs0.24 314027 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9588 Å2 / ksol: 0.365621 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1-13.89 Å20 Å2-3.85 Å2
2---26.95 Å20 Å2
3---13.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49548 0 234 1332 51114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 2649 5 %
Rwork0.346 49901 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4fel.par

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