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- PDB-4i6j: A ubiquitin ligase-substrate complex -

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Basic information

Entry
Database: PDB / ID: 4i6j
TitleA ubiquitin ligase-substrate complex
Components
  • Cryptochrome-2
  • F-box/LRR-repeat protein 3
  • S-phase kinase-associated protein 1
KeywordsTRANSCRIPTION / Circadian Clock / Ubiquitination / LRR / F-box / Photolyase fold / Periods / Nucleus
Function / homology
Function and homology information


regulation of sodium-dependent phosphate transport / Cry-Per complex / negative regulation of glucocorticoid secretion / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / F-box domain binding / negative regulation of circadian rhythm / PcG protein complex / lipid storage / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex ...regulation of sodium-dependent phosphate transport / Cry-Per complex / negative regulation of glucocorticoid secretion / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / F-box domain binding / negative regulation of circadian rhythm / PcG protein complex / lipid storage / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / protein phosphatase inhibitor activity / ubiquitin ligase complex scaffold activity / entrainment of circadian clock by photoperiod / Prolactin receptor signaling / Association of TriC/CCT with target proteins during biosynthesis / cullin family protein binding / response to light stimulus / photoreceptor activity / protein monoubiquitination / ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / phosphatase binding / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / FAD binding / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / molecular function activator activity / nuclear receptor binding / response to activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / response to insulin / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / circadian regulation of gene expression / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Iron uptake and transport / Negative regulation of NOTCH4 signaling / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of circadian rhythm / protein destabilization / beta-catenin binding / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / kinase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / circadian rhythm / Orc1 removal from chromatin / protein import into nucleus / protein polyubiquitination / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / rhythmic process / : / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / glucose homeostasis / Downstream TCR signaling / single-stranded DNA binding / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / transcription cis-regulatory region binding / nuclear speck / protein ubiquitination / nuclear body / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / centrosome / protein kinase binding / negative regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Monooxygenase - #50 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / A Receptor for Ubiquitination Targets / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / F-box-like domain superfamily / F-box-like ...Monooxygenase - #50 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / A Receptor for Ubiquitination Targets / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / F-box domain / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Monooxygenase / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Alpha-Beta Horseshoe / HUPs / SKP1/BTB/POZ domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-phase kinase-associated protein 1 / Cryptochrome-2 / F-box/LRR-repeat protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.7 Å
AuthorsXing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N.
CitationJournal: Nature / Year: 2013
Title: SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket.
Authors: Xing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Cryptochrome-2
B: F-box/LRR-repeat protein 3
C: S-phase kinase-associated protein 1


Theoretical massNumber of molelcules
Total (without water)129,2933
Polymers129,2933
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-53 kcal/mol
Surface area44730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.389, 125.389, 145.712
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Cryptochrome-2


Mass: 61840.605 Da / Num. of mol.: 1 / Fragment: UNP residues 1-544
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry2, Kiaa0658 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R194
#2: Protein F-box/LRR-repeat protein 3 / F-box and leucine-rich repeat protein 3A / F-box/LRR-repeat protein 3A


Mass: 48772.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXL3, FBL3A, FBXL3A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UKT7
#3: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II ...Cyclin-A/CDK2-associated protein p19 / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B / p19A / p19skp1


Mass: 18679.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63208
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M ammonium citrate, 13-14% PEG3350 7% Acetonitrile, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 36840 / Num. obs: 36840 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 28.03
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 4.4 / Rsym value: 0.356 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: molecular replacement-SAD / Resolution: 2.7→47.522 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 29.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2653 1859 5.05 %
Rwork0.2026 --
obs0.2058 36840 99.84 %
all-36840 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5192 Å2-0 Å2-0 Å2
2--3.5192 Å20 Å2
3----7.0384 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8279 0 0 156 8435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098488
X-RAY DIFFRACTIONf_angle_d1.2911507
X-RAY DIFFRACTIONf_dihedral_angle_d17.5793139
X-RAY DIFFRACTIONf_chiral_restr0.0881259
X-RAY DIFFRACTIONf_plane_restr0.0051471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7730.31951380.25792673X-RAY DIFFRACTION100
2.773-2.85460.39381430.25382683X-RAY DIFFRACTION100
2.8546-2.94670.34881470.25942624X-RAY DIFFRACTION100
2.9467-3.0520.3721410.26712698X-RAY DIFFRACTION100
3.052-3.17420.34041380.24892626X-RAY DIFFRACTION100
3.1742-3.31860.33421340.24292711X-RAY DIFFRACTION100
3.3186-3.49360.33161450.22642666X-RAY DIFFRACTION100
3.4936-3.71240.30011420.20272662X-RAY DIFFRACTION100
3.7124-3.99890.24831480.1862682X-RAY DIFFRACTION100
3.9989-4.4010.22861640.17722676X-RAY DIFFRACTION100
4.401-5.03730.21571240.16162749X-RAY DIFFRACTION100
5.0373-6.3440.20851440.18982729X-RAY DIFFRACTION100
6.344-47.5290.19611510.1742802X-RAY DIFFRACTION98

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