[English] 日本語
Yorodumi
- PDB-4i6j: A ubiquitin ligase-substrate complex -

+
Open data


ID or keywords:

Loading...

-
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 / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / F-box domain binding / negative regulation of circadian rhythm / PcG protein complex / lipid storage / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus ...regulation of sodium-dependent phosphate transport / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / F-box domain binding / negative regulation of circadian rhythm / PcG protein complex / lipid storage / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / entrainment of circadian clock by photoperiod / Prolactin receptor signaling / protein monoubiquitination / Association of TriC/CCT with target proteins during biosynthesis / cullin family protein binding / photoreceptor activity / response to light stimulus / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / phosphatase binding / Nuclear events stimulated by ALK signaling in cancer / ubiquitin ligase complex / FAD binding / Regulation of BACH1 activity / post-translational protein modification / MAP3K8 (TPL2)-dependent MAPK1/3 activation / response to activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / molecular function activator activity / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / nuclear receptor binding / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / circadian regulation of gene expression / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / protein destabilization / response to insulin / Degradation of beta-catenin by the destruction complex / regulation of circadian rhythm / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / beta-catenin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / kinase binding / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / Orc1 removal from chromatin / protein import into nucleus / circadian rhythm / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / rhythmic process / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / glucose homeostasis / Downstream TCR signaling / single-stranded DNA binding / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / protein ubiquitination / nuclear body / transcription cis-regulatory region binding / regulation of cell cycle / nuclear speck / 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 / DNA binding / extracellular region / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Monooxygenase - #50 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / A Receptor for Ubiquitination Targets / F-box-like domain superfamily / F-box-like ...Monooxygenase - #50 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 / DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #80 / Cryptochrome/DNA photolyase class 1 / Cryptochrome/DNA photolyase, FAD-binding domain / FAD binding domain of DNA photolyase / A Receptor for Ubiquitination Targets / 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 / F-box domain / DNA photolyase, N-terminal / Cryptochrome/photolyase, N-terminal domain superfamily / DNA photolyase / Photolyase/cryptochrome alpha/beta domain profile. / Cryptochrome/DNA photolyase, FAD-binding domain-like superfamily / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Monooxygenase / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more