- PDB-5vzt: Crystal structure of the Skp1-FBXO31 complex -
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Basic information
Entry
Database: PDB / ID: 5vzt
Title
Crystal structure of the Skp1-FBXO31 complex
Components
F-box only protein 31
S-phase kinase-associated protein 1
Keywords
CELL CYCLE / ubiquitin ligase
Function / homology
Function and homology information
F-box domain binding / PcG protein complex / anaphase-promoting complex-dependent catabolic process / positive regulation of neuron migration / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / positive regulation of dendrite morphogenesis / SCF ubiquitin ligase complex ...F-box domain binding / PcG protein complex / anaphase-promoting complex-dependent catabolic process / positive regulation of neuron migration / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / positive regulation of dendrite morphogenesis / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / mitotic G1 DNA damage checkpoint signaling / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / cyclin binding / 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 / 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 / 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 / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / Circadian Clock / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / mitotic cell cycle / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin remodeling / protein domain specific binding / centrosome / neuronal cell body / DNA damage response / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function
F-box only protein 31/39 / Cyclin D1 binding domain / 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 only protein 31/39 / Cyclin D1 binding domain / 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 / 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 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / PHOSPHATE ION / S-phase kinase-associated protein 1 / F-box only protein 31 Similarity search - Component
Biological species
Homo sapiens (human)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
S-phasekinase-associatedprotein1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / 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 polypeptide 1-like / p19skp1
Mass: 16827.127 Da / Num. of mol.: 2 / Mutation: P2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P63208
#2: Protein
F-boxonlyprotein31
Mass: 55730.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO31, FBX14, FBX31, PP2386 Details (production host): Modified pET15b vector with a StrepII tag Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5XUX0
Method to determine structure: SAD / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 24.203 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.432 / ESU R Free: 0.284 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2423
2777
5.1 %
RANDOM
Rwork
0.1952
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obs
0.1976
51977
98.89 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
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