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- PDB-2e33: Structural basis for selection of glycosylated substrate by SCFFb... -

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Basic information

Entry
Database: PDB / ID: 2.0E+33
TitleStructural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase
Components
  • F-box only protein 2
  • Ribonuclease pancreatic
KeywordsLIGASE/HYDROLASE / ubiquitin / SCF / Fbs1 / RNaseB / LIGASE-HYDROLASE COMPLEX
Function / homology
Function and homology information


extrinsic component of postsynaptic membrane / denatured protein binding / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / glycoprotein catabolic process / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / SCF ubiquitin ligase complex / pancreatic ribonuclease / ribonuclease A activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ...extrinsic component of postsynaptic membrane / denatured protein binding / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / glycoprotein catabolic process / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / SCF ubiquitin ligase complex / pancreatic ribonuclease / ribonuclease A activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / regulation of protein ubiquitination / RNA nuclease activity / ERAD pathway / amyloid-beta binding / ubiquitin-dependent protein catabolic process / carbohydrate binding / nucleic acid binding / dendritic spine / lyase activity / defense response to Gram-positive bacterium / protein ubiquitination / negative regulation of cell population proliferation / glutamatergic synapse / endoplasmic reticulum / extracellular region / cytosol / cytoplasm
Similarity search - Function
F-box associated (FBA) domain / F-box only protein / F-box associated region / F-box-associated (FBA) domain profile. / F-box associated region / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / P-30 Protein ...F-box associated (FBA) domain / F-box only protein / F-box associated region / F-box-associated (FBA) domain profile. / F-box associated region / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Roll / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ribonuclease pancreatic / F-box only protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMizushima, T. / Yoshida, Y. / Kumanomidou, T. / Hasegawa, Y. / Yamane, T. / Tanaka, K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for the selection of glycosylated substrates by SCFFbs1 ubiquitin ligase
Authors: Mizushima, T. / Yoshida, Y. / Kumanomidou, T. / Hasegawa, Y. / Suzuki, A. / Yamane, T. / Tanaka, K.
History
DepositionNov 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 26, 2014Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box only protein 2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2133
Polymers36,3022
Non-polymers9111
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.314, 148.314, 148.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein F-box only protein 2 / Fbs1


Mass: 22593.631 Da / Num. of mol.: 1 / Fragment: Residues 105-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q80UW2
#2: Protein Ribonuclease pancreatic / RNase 1 / RNase A / Ribonuclease B


Mass: 13708.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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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: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0% (v/v) PEG 400, 0.1M HEPES, 2.1M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jul 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→149.1 Å / Num. obs: 15839 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 5.2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UMH

1umh


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.881 / SU B: 11.824 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28807 790 5 %RANDOM
Rwork0.21618 ---
obs0.2198 15049 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.8 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 61 0 2423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0212486
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5081.9493379
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8065297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.0724.597124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.38615391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.0211514
X-RAY DIFFRACTIONr_chiral_restr0.1580.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021899
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.21106
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.21718
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1871.51518
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0422385
X-RAY DIFFRACTIONr_scbond_it3.00531123
X-RAY DIFFRACTIONr_scangle_it4.6444.5994
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 54 -
Rwork0.258 1064 -
obs--97.9 %

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