- PDB-2vt8: Structure of a conserved dimerisation domain within Fbox7 and PI31 -
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Basic information
Entry
Database: PDB / ID: 2vt8
Title
Structure of a conserved dimerisation domain within Fbox7 and PI31
Components
PROTEASOME INHIBITOR PI31 SUBUNIT
Keywords
HYDROLASE INHIBITOR / POLYMORPHISM
Function / homology
Function and homology information
negative regulation of proteasomal protein catabolic process / proteasome core complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / endopeptidase inhibitor activity / proteasome binding / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin ...negative regulation of proteasomal protein catabolic process / proteasome core complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / endopeptidase inhibitor activity / proteasome binding / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / 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 / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / protein heterodimerization activity / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / nucleoplasm / membrane / cytosol Similarity search - Function
Protein Transport Mog1p; Chain A - #30 / PI31 proteasome regulator, C-terminal / Proteasome inhibitor PI31-like / PI31 proteasome regulator / PI31 proteasome regulator, N-terminal / PI31 proteasome regulator N-terminal / Protein Transport Mog1p; Chain A / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 2.6→28.1 Å / Num. obs: 9607 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.1
Reflection shell
Resolution: 2.6→2.74 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.1 / % possible all: 97.9
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
MOSFLM
datareduction
SCALA
datascaling
MOLREP
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: PART-REFINED MODEL OF A L7M SEMET DERIVATIVE OBTAINED BY SAD PHASING Resolution: 2.6→28.09 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.888 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 1.262 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.256
459
4.8 %
RANDOM
Rwork
0.203
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obs
0.206
9115
99.9 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK