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- PDB-5vzu: Crystal structure of the Skp1-FBXO31-cyclin D1 complex -

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Basic information

Entry
Database: PDB / ID: 5vzu
TitleCrystal structure of the Skp1-FBXO31-cyclin D1 complex
Components
  • Cyclin D1
  • F-box only protein 31
  • S-phase kinase-associated protein 1
KeywordsCELL CYCLE / ubiquitin ligase
Function / homology
Function and homology information


cyclin D1-CDK4 complex / cyclin D1-CDK6 complex / re-entry into mitotic cell cycle / Drug-mediated inhibition of CDK4/CDK6 activity / RUNX3 regulates WNT signaling / positive regulation of mammary gland epithelial cell proliferation / response to leptin / F-box domain binding / anaphase-promoting complex-dependent catabolic process / Transcriptional regulation by RUNX2 ...cyclin D1-CDK4 complex / cyclin D1-CDK6 complex / re-entry into mitotic cell cycle / Drug-mediated inhibition of CDK4/CDK6 activity / RUNX3 regulates WNT signaling / positive regulation of mammary gland epithelial cell proliferation / response to leptin / F-box domain binding / anaphase-promoting complex-dependent catabolic process / Transcriptional regulation by RUNX2 / PcG protein complex / Leydig cell differentiation / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / proline-rich region binding / cyclin-dependent protein serine/threonine kinase activator activity / Regulation of RUNX1 Expression and Activity / response to iron ion / mammary gland epithelial cell proliferation / cyclin-dependent protein serine/threonine kinase regulator activity / response to UV-A / SCF ubiquitin ligase complex / response to vitamin E / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / response to corticosterone / negative regulation of epithelial cell differentiation / PTK6 Regulates Cell Cycle / Prolactin receptor signaling / ubiquitin ligase complex scaffold activity / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / microtubule organizing center / Transcriptional Regulation by VENTX / response to magnesium ion / RUNX3 regulates p14-ARF / mammary gland alveolus development / cullin family protein binding / positive regulation of G2/M transition of mitotic cell cycle / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / bicellular tight junction / response to X-ray / protein monoubiquitination / fat cell differentiation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / endoplasmic reticulum unfolded protein response / protein K48-linked ubiquitination / ubiquitin-like ligase-substrate adaptor activity / cyclin-dependent protein kinase holoenzyme complex / : / signal transduction in response to DNA damage / lactation / Nuclear events stimulated by ALK signaling in cancer / mitotic G1 DNA damage checkpoint signaling / transcription repressor complex / liver regeneration / molecular function activator activity / cyclin binding / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / protein serine/threonine kinase activator activity / Ubiquitin-dependent degradation of Cyclin D / 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 / G1/S transition of mitotic cell cycle / Degradation of GLI1 by the proteasome / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / response to calcium ion / 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 / beta-catenin binding / Degradation of beta-catenin by the destruction complex / response to estrogen / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / CLEC7A (Dectin-1) signaling / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / histone deacetylase binding / Wnt signaling pathway / Interleukin-1 signaling / RMTs methylate histone arginines / protein polyubiquitination / Orc1 removal from chromatin / neuron differentiation / Cyclin D associated events in G1 / Regulation of RUNX2 expression and activity / transcription corepressor activity / Regulation of PLK1 Activity at G2/M Transition / response to estradiol / Downstream TCR signaling
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 / 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 only protein 31/39 / Cyclin D1 binding domain / 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 / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / 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 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / SKP1/BTB/POZ domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / G1/S-specific cyclin-D1 / S-phase kinase-associated protein 1 / F-box only protein 31 / Cyclin D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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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
E: Cyclin D1
F: Cyclin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,13718
Polymers149,0576
Non-polymers1,08112
Water1,11762
1
A: S-phase kinase-associated protein 1
B: F-box only protein 31
E: Cyclin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0699
Polymers74,5283
Non-polymers5406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: S-phase kinase-associated protein 1
D: F-box only protein 31
F: Cyclin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0699
Polymers74,5283
Non-polymers5406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.679, 156.235, 155.522
Angle α, β, γ (deg.)90.000, 104.210, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1010 - 1066
2115C1010 - 1066
1215A1083 - 1160
2215C1083 - 1160
1125B12 - 203
2125D12 - 203
1225B220 - 487
2225D220 - 487
1133E288 - 293
2133F288 - 293

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.163247, 0.0554, -0.985029), (0.070896, -0.9965, -0.044296), (-0.984035, -0.062604, -0.166603)-21.04232, -0.63435, 76.774117

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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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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Cyclin D1


Mass: 1971.019 Da / Num. of mol.: 2 / Fragment: UNP residues 109-125 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H014, UniProt: P24385*PLUS

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Non-polymers , 3 types, 74 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN
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: 3.47 Å3/Da / Density % sol: 64.55 %
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: Feb 20, 2014 / 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: 55014 / % possible obs: 99.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.059 / Χ2: 0.906 / Net I/σ(I): 9.7 / Num. measured all: 416593
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
2.7-2.756.60.6960.712190.9
2.75-2.86.90.6330.722194.5
2.8-2.857.10.5970.74198
2.85-2.917.40.4780.747199.9
2.91-2.977.60.3850.7531100
2.97-3.047.70.3220.7741100
3.04-3.127.70.2590.7921100
3.12-3.27.70.2010.7721100
3.2-3.37.70.1510.8111100
3.3-3.47.70.1270.8331100
3.4-3.527.80.0940.841100
3.52-3.667.70.0790.8641100
3.66-3.837.80.0630.8921100
3.83-4.037.70.0560.9771100
4.03-4.297.70.0511.2431100
4.29-4.627.70.0511.2231100
4.62-5.087.70.0461.1041100
5.08-5.817.70.0391.0491100
5.81-7.327.70.0361.0711100
7.32-507.60.0271.095198.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VZT

5vzt


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 22.513 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.394 / ESU R Free: 0.272 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2674 4.9 %RANDOM
Rwork0.1804 ---
obs0.1829 52339 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 238.66 Å2 / Biso mean: 89.949 Å2 / Biso min: 24.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å2-0 Å2-1.36 Å2
2---1.77 Å20 Å2
3---1.47 Å2
Refinement stepCycle: final / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9191 0 52 62 9305
Biso mean--116.35 62.79 -
Num. residues----1138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0199519
X-RAY DIFFRACTIONr_bond_other_d0.0010.029005
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.96312885
X-RAY DIFFRACTIONr_angle_other_deg0.802320728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65651143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22323.521463
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.676151661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3711578
X-RAY DIFFRACTIONr_chiral_restr0.080.21391
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022221
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A794MEDIUM POSITIONAL0.260.5
1A1350LOOSE POSITIONAL0.415
1A794MEDIUM THERMAL15.262
1A1350LOOSE THERMAL15.4210
2B2337MEDIUM POSITIONAL0.280.5
2B4029LOOSE POSITIONAL0.385
2B2337MEDIUM THERMAL7.542
2B4029LOOSE THERMAL8.4310
3E64LOOSE POSITIONAL0.695
3E35TIGHT THERMAL17.490.5
3E64LOOSE THERMAL10.7810
LS refinement shellResolution: 2.702→2.772 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 198 -
Rwork0.3 3507 -
all-3705 -
obs--90.88 %
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)
13.35810.51121.38371.4381-0.07961.76940.05920.2990.3525-0.1562-0.2193-0.0859-0.03220.26850.16010.04360.02970.03660.08820.04650.0958-2.7414-26.963158.1962
21.0871-1.75490.27972.9129-0.42630.3636-0.1073-0.0350.08790.23970.1409-0.142-0.077-0.0274-0.03360.15060.0488-0.06360.10660.04950.1429-42.6631-2.758256.3568
31.97360.18321.22252.03250.6383.9686-0.33551.1404-0.1013-0.04310.2031-0.1714-0.36631.77810.13250.4884-0.3936-0.24721.08890.12550.216619.324128.4883-14.0605
41.7551-0.23610.73861.389-1.15193.2226-0.00440.4564-0.4644-0.6512-0.07240.4220.39410.21640.07690.40110.0644-0.2070.1991-0.13710.366315.95212.867225.6754
53.96483.9601-7.01753.9809-7.018412.42930.3680.53540.40610.38150.42320.4259-0.7119-0.9274-0.79120.2190.11070.08180.34450.05070.2745-59.811117.534352.6676
69.39629.3217-7.885713.8795-14.205115.42470.0158-1.24990.2848-0.60950.03930.120.8061-0.7419-0.05510.297-0.07490.06340.5788-0.01730.239420.712-17.050141.4879
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
5X-RAY DIFFRACTION5E287 - 293
6X-RAY DIFFRACTION6F290 - 293

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