[English] 日本語
Yorodumi
- PDB-3l2o: Structure-Based Mechanism of Dimerization-Dependent Ubiquitinatio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l2o
TitleStructure-Based Mechanism of Dimerization-Dependent Ubiquitination by the SCFFbx4 Ubiquitin Ligase
Components
  • F-box only protein 4
  • S-phase kinase-associated protein 1
KeywordsPROTEIN BINDING/CELL CYCLE / small G protein fold / Ubl conjugation pathway / ubiquitin protein ligase / PROTEIN BINDING-CELL CYCLE complex
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / F-box domain binding / common myeloid progenitor cell proliferation / PcG protein complex / cellular homeostasis / regulation of DNA damage checkpoint / 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 ...positive regulation of protein polyubiquitination / F-box domain binding / common myeloid progenitor cell proliferation / PcG protein complex / cellular homeostasis / regulation of DNA damage checkpoint / 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 / negative regulation of protein localization to nucleus / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / post-transcriptional regulation of gene expression / Prolactin receptor signaling / protein monoubiquitination / Association of TriC/CCT with target proteins during biosynthesis / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / ubiquitin ligase complex / negative regulation of fibroblast proliferation / positive regulation of telomere maintenance via telomerase / telomere maintenance / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / molecular function activator activity / Vpu mediated degradation of CD4 / cellular response to ionizing radiation / Dectin-1 mediated noncanonical NF-kB signaling / 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 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / protein destabilization / regulation of protein stability / Degradation of beta-catenin by the destruction complex / 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 / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / Orc1 removal from chromatin / ubiquitin-protein transferase activity / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / ubiquitin protein ligase activity / Regulation of PLK1 Activity at G2/M Transition / cellular senescence / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Downstream TCR signaling / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin remodeling / protein domain specific binding / centrosome / protein homodimerization activity / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
F-box only protein 4 / F-box domain / Monooxygenase - #50 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily ...F-box only protein 4 / F-box domain / Monooxygenase - #50 / A Receptor for Ubiquitination Targets / F-box domain profile. / 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 / 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 / SKP1/BTB/POZ domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-phase kinase-associated protein 1 / F-box only protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLi, Y. / Hao, B.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural basis of dimerization-dependent ubiquitination by the SCF(Fbx4) ubiquitin ligase.
Authors: Li, Y. / Hao, B.
History
DepositionDec 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-phase kinase-associated protein 1
B: F-box only protein 4


Theoretical massNumber of molelcules
Total (without water)52,6762
Polymers52,6762
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-23 kcal/mol
Surface area23240 Å2
MethodPISA
2
A: S-phase kinase-associated protein 1
B: F-box only protein 4

A: S-phase kinase-associated protein 1
B: F-box only protein 4


Theoretical massNumber of molelcules
Total (without water)105,3524
Polymers105,3524
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area8730 Å2
ΔGint-70 kcal/mol
Surface area43590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.194, 92.194, 148.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein S-phase kinase-associated protein 1 / / Cyclin A/CDK2-associated protein p19 / p19skp1 / p19A / RNA polymerase II elongation factor-like ...Cyclin A/CDK2-associated protein p19 / p19skp1 / p19A / RNA polymerase II elongation factor-like protein / Organ of Corti protein 2 / OCP-2 / OCP-II / Transcription elongation factor B / SIII


Mass: 16827.127 Da / Num. of mol.: 1
Mutation: deletion: 38-43, 70-81; P2A; insertion: GGSG between 69 and 82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EMC19, OCP2, SKP1, SKP1A, TCEB1L / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63208
#2: Protein F-box only protein 4


Mass: 35848.684 Da / Num. of mol.: 1 / Fragment: Fbx4 residues 55-387 / Mutation: deletion: 150-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBX4, FBXO4 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKT5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.45 Å3/Da / Density % sol: 64.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5-2 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X3A11.0721
SYNCHROTRONNSLS X29A21.0809
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDApr 17, 2008mirrors
ADSC QUANTUM 3152CCDOct 3, 2008mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1YALE MIRRORSSINGLE WAVELENGTHMx-ray1
2YALE MIRRORSSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.07211
21.08091
ReflectionResolution: 2.8→50 Å / Num. all: 17477 / Num. obs: 17477 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 84.1 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 31.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1843 / Rsym value: 0.856 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / SU B: 38.305 / SU ML: 0.333 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.678 / ESU R Free: 0.372
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29488 915 5 %RANDOM
Rwork0.24945 ---
obs0.25171 17477 99.52 %-
all-17477 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.752 Å2
Baniso -1Baniso -2Baniso -3
1-3.89 Å21.95 Å20 Å2
2--3.89 Å20 Å2
3----5.84 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 0 76 3425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223425
X-RAY DIFFRACTIONr_bond_other_d0.0020.022283
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.9584651
X-RAY DIFFRACTIONr_angle_other_deg1.02635598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0475412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.125.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72715589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8731514
X-RAY DIFFRACTIONr_chiral_restr0.0650.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02653
X-RAY DIFFRACTIONr_mcbond_it0.561.52090
X-RAY DIFFRACTIONr_mcbond_other0.0891.5835
X-RAY DIFFRACTIONr_mcangle_it1.07323392
X-RAY DIFFRACTIONr_scbond_it1.46131335
X-RAY DIFFRACTIONr_scangle_it2.4194.51259
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.466 82 -
Rwork0.388 1240 -
obs-1240 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5617-5.3184-0.77267.2631.64736.5632-0.862-1.8277-1.15391.13970.64431.11211.3584-0.42940.21780.51820.20840.04650.84510.12720.4067102.149429.175463.7807
27.4704-3.4441-2.011612.27161.92987.73160.1462-0.1445-0.0651-0.25260.11330.61050.2825-0.2117-0.25950.12840.152-0.10120.3165-0.06630.1307108.231838.030750.0442
36.7175-0.9561-5.05194.84372.452611.3841-0.28870.0887-0.5859-0.43750.3458-1.05570.27771.4387-0.05710.28610.1519-0.07260.7099-0.18170.5478120.629929.084638.7606
42.85131.2654.58241.56161.583510.45380.24810.4254-0.2980.20250.2755-0.38211.20260.9713-0.52360.32960.2616-0.06070.415-0.1230.3318112.37724.239833.1861
59.4302-1.35971.683813.4489-1.509113.22620.29210.0335-0.87440.12250.0036-0.17531.46170.2469-0.29560.48910.1695-0.06690.5733-0.10740.4996105.534418.612423.692
68.37350.5963-0.42442.60131.791712.05980.0046-1.03210.11360.68310.07520.11590.2977-0.3244-0.07970.4890.1055-0.08340.17410.01150.2665125.495910.50760.6525
74.0039-0.35061.66944.11820.73647.7440.0541-0.48310.03510.63680.02950.32230.4398-0.8983-0.08360.2607-0.03320.02680.12920.00240.1783115.920710.1495-8.7059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1002 - 1064
2X-RAY DIFFRACTION2A1065 - 1106
3X-RAY DIFFRACTION3A1107 - 1160
4X-RAY DIFFRACTION4B54 - 119
5X-RAY DIFFRACTION5B120 - 174
6X-RAY DIFFRACTION6B175 - 275
7X-RAY DIFFRACTION7B276 - 383

+
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