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- PDB-2rj2: Crystal Structure of the Sugar Recognizing SCF Ubiquitin Ligase a... -

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Basic information

Entry
Database: PDB / ID: 2rj2
TitleCrystal Structure of the Sugar Recognizing SCF Ubiquitin Ligase at 1.7 Resolution
ComponentsF-box only protein 2
KeywordsLIGASE / UBIQUITIN / SCF / UBIQUITIN LIGASE / LECTIN / Ubl conjugation pathway
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 / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ERAD pathway / regulation of protein ubiquitination ...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 / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ERAD pathway / regulation of protein ubiquitination / ubiquitin protein ligase activity / amyloid-beta binding / ubiquitin-dependent protein catabolic process / carbohydrate binding / dendritic spine / protein ubiquitination / negative regulation of cell population proliferation / glutamatergic synapse / endoplasmic reticulum / 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 / Galactose-binding domain-like ...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 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / F-box only protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVaijayanthimala, S. / Velmurugan, D. / Mizushima, T. / Yamane, T. / Yoshida, Y. / Tanaka, K.
Citation
Journal: To be Published
Title: Crystal Structure of the Sugar Recognizing SCF Ubiquitin Ligase at 1.7 Resolution
Authors: Vaijayanthimala, S. / Velmurugan, D. / Mizushima, T. / Yamane, T. / Yoshida, Y. / Tanaka, K.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis of sugar-recognizing ubiquitin ligase
Authors: Mizushima, T. / Hirao, T. / Yoshida, Y. / Lee, S.J. / Chiba, T. / Iwai, K. / Yamaguchi, Y. / Kato, K. / Tsukihara, T. / Tanaka, K.
History
DepositionOct 14, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,2463
Polymers21,1521
Non-polymers942
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.760, 61.760, 115.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-544-

HOH

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Components

#1: Protein F-box only protein 2


Mass: 21152.205 Da / Num. of mol.: 1 / Fragment: SBD DOMAIN. UNP residues 117-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fbxo2, Fbx2 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) / References: UniProt: Q80UW2, ubiquitin-protein ligase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE DIFFERENCES BETWEEN THE REPORTED SEQRES AND THE DATABASE SEQUENCE. THE DEPOSITORS BELIEVE ...THERE ARE DIFFERENCES BETWEEN THE REPORTED SEQRES AND THE DATABASE SEQUENCE. THE DEPOSITORS BELIEVE THAT THESE RESIDUES ARE VALIANTS AT THE POSITIONS.

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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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS, 0.1%(v/v) PEG 400, 0.01M NICKEL CHLORIDE, 1.7M AMMONIUM SULFATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 23, 2006
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 27682 / Num. obs: 27682 / % possible obs: 97.4 % / Rsym value: 0.072
Reflection shellResolution: 1.7→1.79 Å / Rsym value: 0.241 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UMH

1umh


Resolution: 1.7→19.91 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.81 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21482 2749 10.1 %RANDOM
Rwork0.18533 ---
all0.18834 ---
obs0.18834 24567 95.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.937 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 2 256 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211536
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9192083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5045184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23623.97683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08115238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0151510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021210
X-RAY DIFFRACTIONr_nbd_refined0.2170.2732
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21033
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.2197
X-RAY DIFFRACTIONr_metal_ion_refined0.0370.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.242
X-RAY DIFFRACTIONr_mcbond_it0.8661.5924
X-RAY DIFFRACTIONr_mcangle_it1.36121452
X-RAY DIFFRACTIONr_scbond_it1.9863723
X-RAY DIFFRACTIONr_scangle_it3.0124.5631
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 184 -
Rwork0.331 1874 -
obs--99.09 %

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