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- PDB-5v4b: Crystal structure of the Skp1-FBXW7-DISC1 complex -

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Basic information

Entry
Database: PDB / ID: 5v4b
TitleCrystal structure of the Skp1-FBXW7-DISC1 complex
Components
  • DISC1 peptide
  • F-box/WD repeat-containing protein 7
  • S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
KeywordsTRANSCRIPTION / Ubiquitin ligase/psychiatric disorders / TRANSCRIPTION-CELL C complex
Function / homology
Function and homology information


pyramidal neuron migration to cerebral cortex / negative regulation of SREBP signaling pathway / negative regulation of triglyceride biosynthetic process / negative regulation of hepatocyte proliferation / cell proliferation in forebrain / central region of growth cone / regulation of lipid storage / mitochondrial calcium ion homeostasis / Parkin-FBXW7-Cul1 ubiquitin ligase complex / ubiquitin recycling ...pyramidal neuron migration to cerebral cortex / negative regulation of SREBP signaling pathway / negative regulation of triglyceride biosynthetic process / negative regulation of hepatocyte proliferation / cell proliferation in forebrain / central region of growth cone / regulation of lipid storage / mitochondrial calcium ion homeostasis / Parkin-FBXW7-Cul1 ubiquitin ligase complex / ubiquitin recycling / ubiquitin-protein transferase activator activity / regulation of dendritic spine development / F-box domain binding / regulation of mitophagy / regulation of cell cycle G1/S phase transition / negative regulation of osteoclast development / PcG protein complex / phosphothreonine residue binding / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / regulation of synapse maturation / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / maintenance of protein location in nucleus / intermediate filament cytoskeleton / positive regulation of proteasomal protein catabolic process / non-motile cilium assembly / vasculature development / positive regulation of ubiquitin-dependent protein catabolic process / dynein complex / protein localization to centrosome / regulation of postsynapse organization / kinesin complex / positive regulation of protein targeting to mitochondrion / SCF ubiquitin ligase complex / sister chromatid cohesion / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cell-matrix adhesion / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / positive regulation of neuroblast proliferation / Prolactin receptor signaling / ciliary base / ubiquitin ligase complex scaffold activity / detection of temperature stimulus involved in sensory perception of pain / Association of TriC/CCT with target proteins during biosynthesis / lipid homeostasis / TOR signaling / microtubule organizing center / cullin family protein binding / response to electrical stimulus / cilium assembly / negative regulation of Notch signaling pathway / protein monoubiquitination / kinesin binding / canonical Wnt signaling pathway / positive regulation of Wnt signaling pathway / positive regulation of axon extension / regulation of synaptic transmission, glutamatergic / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / cyclin binding / Regulation of BACH1 activity / molecular function activator activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / ubiquitin binding / positive regulation of protein ubiquitination / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / positive regulation of neuron projection development / neuron cellular homeostasis / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / beta-catenin binding / GABA-ergic synapse / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / microtubule cytoskeleton organization / Interleukin-1 signaling / neuron migration / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / synaptic vesicle / cellular response to UV
Similarity search - Function
Disrupted in schizophrenia 1 / Monooxygenase - #50 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain ...Disrupted in schizophrenia 1 / Monooxygenase - #50 / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like / F-box-like domain superfamily / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Monooxygenase / 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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / S-phase kinase-associated protein 1 / F-box/WD repeat-containing protein 7 / Disrupted in schizophrenia 1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, Y. / Baillie, G.S. / Hao, B.
CitationJournal: Mol. Psychiatry / Year: 2018
Title: FBXW7 regulates DISC1 stability via the ubiquitin-proteosome system.
Authors: Yalla, K. / Elliott, C. / Day, J.P. / Findlay, J. / Barratt, S. / Hughes, Z.A. / Wilson, L. / Whiteley, E. / Popiolek, M. / Li, Y. / Dunlop, J. / Killick, R. / Adams, D.R. / Brandon, N.J. / ...Authors: Yalla, K. / Elliott, C. / Day, J.P. / Findlay, J. / Barratt, S. / Hughes, Z.A. / Wilson, L. / Whiteley, E. / Popiolek, M. / Li, Y. / Dunlop, J. / Killick, R. / Adams, D.R. / Brandon, N.J. / Houslay, M.D. / Hao, B. / Baillie, G.S.
History
DepositionMar 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
B: F-box/WD repeat-containing protein 7
C: DISC1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,60713
Polymers68,6733
Non-polymers93410
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-122 kcal/mol
Surface area26790 Å2
MethodPISA
2
A: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
B: F-box/WD repeat-containing protein 7
C: DISC1 peptide
hetero molecules

A: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
B: F-box/WD repeat-containing protein 7
C: DISC1 peptide
hetero molecules

A: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
B: F-box/WD repeat-containing protein 7
C: DISC1 peptide
hetero molecules

A: S-phase kinase-associated protein 1,S-phase kinase-associated protein 1
B: F-box/WD repeat-containing protein 7
C: DISC1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,42752
Polymers274,69212
Non-polymers3,73540
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_554y,x,-z-11
Buried area34550 Å2
ΔGint-545 kcal/mol
Surface area97980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.514, 233.514, 108.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-3015-

HOH

21B-3026-

HOH

31B-3048-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein S-phase kinase-associated protein 1,S-phase kinase-associated protein 1 / 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: 16841.152 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 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63208
#2: Protein F-box/WD repeat-containing protein 7 / Archipelago homolog / hAgo / F-box and WD-40 domain-containing protein 7 / F-box protein FBX30 / ...Archipelago homolog / hAgo / F-box and WD-40 domain-containing protein 7 / F-box protein FBX30 / SEL-10 / hCdc4


Mass: 50150.230 Da / Num. of mol.: 1 / Fragment: UNP residues 183-626
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXW7, FBW7, FBX30, SEL10 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q969H0

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide DISC1 peptide


Mass: 1681.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NRI5*PLUS

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Non-polymers , 3 types, 177 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.43 Å3/Da / Density % sol: 77.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 100 mM Hepes, 1.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→42.93 Å / Num. obs: 45981 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.103 / Χ2: 1.016 / Net I/σ(I): 10.2 / Num. measured all: 279701
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.6-2.645.70.6050.84199.4
2.64-2.695.70.50.883199.6
2.69-2.745.80.4530.92199.2
2.74-2.85.80.3850.943199.6
2.8-2.865.90.3431.014199.3
2.86-2.935.90.2981.02199.9
2.93-35.90.2641.015199.6
3-3.0860.2121.095199.8
3.08-3.1760.181.127199.9
3.17-3.2860.1561.004199.9
3.28-3.3960.1330.947199.9
3.39-3.536.10.1210.9921100
3.53-3.696.20.1071.0511100
3.69-3.886.40.0991.0461100
3.88-4.136.50.090.9311100
4.13-4.456.50.0831.1141100
4.45-4.896.50.0781.1281100
4.89-5.66.40.06811100
5.6-7.056.30.061.0731100
7.05-506.20.0381.11199.2

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OVP

2ovp


Resolution: 2.6→42.93 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.104 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.194 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 2328 5.1 %RANDOM
Rwork0.1837 ---
obs0.1854 43643 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 222.9 Å2 / Biso mean: 57.154 Å2 / Biso min: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å2-0 Å20 Å2
2--1.35 Å20 Å2
3----2.7 Å2
Refinement stepCycle: final / Resolution: 2.6→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 50 167 4862
Biso mean--87.64 45.71 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194831
X-RAY DIFFRACTIONr_bond_other_d0.0010.024536
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.9526579
X-RAY DIFFRACTIONr_angle_other_deg0.877310416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9025607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21924.293205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.94715814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7531528
X-RAY DIFFRACTIONr_chiral_restr0.1050.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021090
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 181 -
Rwork0.297 3163 -
all-3344 -
obs--99.11 %
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)
14.1025-1.1397-1.34991.73760.45831.0158-0.0508-0.509-0.43520.23650.032-0.10310.39580.13490.01880.3777-0.1899-0.07940.32970.11070.6175-0.4909-17.7199-38.8246
21.1223-0.1179-0.48630.3760.42023.02950.10080.25680.27490.1051-0.049-0.08350.0805-0.3665-0.05170.0787-0.0195-0.01560.11830.07880.0977-46.0502-23.812-36.8926
311.08668.00380.697917.53135.54362.259-0.092-0.00730.40230.095-0.18770.23490.1525-0.13460.27970.3815-0.37380.1650.7772-0.07020.5738-66.087-35.2525-28.4131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1002 - 1147
2X-RAY DIFFRACTION2B2263 - 2706
3X-RAY DIFFRACTION3C193 - 201

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