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- PDB-5vzt: Crystal structure of the Skp1-FBXO31 complex -

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Basic information

Entry
Database: PDB / ID: 5vzt
TitleCrystal structure of the Skp1-FBXO31 complex
Components
  • F-box only protein 31
  • S-phase kinase-associated protein 1
KeywordsCELL 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 / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of dendrite morphogenesis / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process ...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 / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of dendrite morphogenesis / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / 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 / cyclin binding / MAP3K8 (TPL2)-dependent MAPK1/3 activation / 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 / protein polyubiquitination / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Downstream TCR signaling / Neddylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin remodeling / protein domain specific binding / centrosome / neuronal cell body / DNA damage response / nucleoplasm / nucleus / cytosol / cytoplasm
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsLi, Y. / Jin, K. / Hao, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099948 United States
Connecticut Regenerative Medicine Research Fund15-RMA-UCHC-04 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of the phosphorylation-independent recognition of cyclin D1 by the SCFFBXO31 ubiquitin ligase.
Authors: Li, Y. / Jin, K. / Bunker, E. / Zhang, X. / Luo, X. / Liu, X. / Hao, B.
History
DepositionMay 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: F-box only protein 31
C: S-phase kinase-associated protein 1
D: F-box only protein 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,31416
Polymers145,1144
Non-polymers1,19912
Water1,47782
1
A: S-phase kinase-associated protein 1
B: F-box only protein 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1578
Polymers72,5572
Non-polymers6006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: S-phase kinase-associated protein 1
D: F-box only protein 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1578
Polymers72,5572
Non-polymers6006
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.521, 156.310, 154.596
Angle α, β, γ (deg.)90.000, 103.620, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12A
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115B12 - 200
2115D12 - 200
1215B220 - 487
2215D220 - 487
1125A1010 - 1068
2125C1010 - 1068
1225A1083 - 1162
2225C1083 - 1162

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.06123, 0.027493, -0.997745), (0.00784, -0.999603, -0.027063), (-0.998093, -0.006165, -0.061421)-17.516171, 0.71553, 74.023277

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein 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: 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-box only protein 31


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

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Non-polymers , 4 types, 94 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsresidues 38-43 deleted, residues 70-83 replaced with GGSGT

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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: 3.55 Å3/Da / Density % sol: 65.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 100 mM sodium citrate (pH 5.3), 0.27 M ammonium acetate, 13-17% MPD, 0.02 M CaCl2
PH range: 5.3-5.5

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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: Jul 12, 2013 / Details: Mini-gap Undulator
RadiationMonochromator: Striped Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 54754 / % possible obs: 99.2 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.069 / Χ2: 0.959 / Net I/σ(I): 11.2 / Num. measured all: 413619
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.7-2.756.40.6470.822191.5
2.75-2.86.70.5940.818194.9
2.8-2.8570.560.832198.3
2.85-2.917.30.4790.838199.7
2.91-2.977.60.4040.8481100
2.97-3.047.70.3330.8661100
3.04-3.127.70.2740.8641100
3.12-3.27.70.2140.8671100
3.2-3.37.70.1680.9161100
3.3-3.47.70.1380.911100
3.4-3.527.80.1050.9631100
3.52-3.667.70.0860.9671100
3.66-3.837.80.0691.0051100
3.83-4.037.70.0580.9881100
4.03-4.297.70.0541.0211100
4.29-4.627.70.0510.9911100
4.62-5.087.70.0461.2761100
5.08-5.817.70.0411.1281100
5.81-7.327.70.0381.0241100
7.32-507.60.0281.132199.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 2777 5.1 %RANDOM
Rwork0.1952 ---
obs0.1976 51977 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 301.13 Å2 / Biso mean: 79.361 Å2 / Biso min: 16 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å2-0.45 Å2
2---2.37 Å20 Å2
3---0.36 Å2
Refinement stepCycle: final / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9054 0 74 82 9210
Biso mean--84.71 55.23 -
Num. residues----1123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0199507
X-RAY DIFFRACTIONr_bond_other_d0.0010.028973
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.96312878
X-RAY DIFFRACTIONr_angle_other_deg0.941320671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.36151151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15223.514461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.753151655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2371577
X-RAY DIFFRACTIONr_chiral_restr0.10.21388
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110688
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022235
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B2300MEDIUM POSITIONAL0.340.5
1B3957LOOSE POSITIONAL0.515
1B2300MEDIUM THERMAL9.952
1B3957LOOSE THERMAL10.4110
2A824MEDIUM POSITIONAL0.290.5
2A1388LOOSE POSITIONAL0.585
2A824MEDIUM THERMAL17.542
2A1388LOOSE THERMAL18.1410
LS refinement shellResolution: 2.701→2.771 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 177 -
Rwork0.339 3457 -
all-3634 -
obs--88.96 %
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)
12.85110.52540.99091.3972-0.12621.2180.0620.27330.3795-0.1353-0.23080.03660.04240.26880.16880.04070.0592-0.0050.12590.03610.1968-1.8884-26.969557.9464
21.0604-1.76070.3383.0432-0.5370.3344-0.1203-0.02620.09110.28410.1642-0.1745-0.0585-0.007-0.04390.13490.0804-0.05820.15150.05520.227-41.8725-2.768156.0885
32.4510.30361.55392.2771.18774.1626-0.30231.18520.005-0.07220.232-0.1638-0.41871.65520.07030.3361-0.3645-0.24210.93040.1650.212119.175728.5979-14.0825
41.6145-0.12060.64251.4901-1.1833.1442-0.05040.3648-0.4392-0.6144-0.0520.36010.47380.24550.10240.31450.0647-0.15290.17-0.12210.353916.43973.103125.5601
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1008 - 1163
2X-RAY DIFFRACTION2B63 - 539
3X-RAY DIFFRACTION3C1008 - 1163
4X-RAY DIFFRACTION4D64 - 539

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