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- PDB-2ast: Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide -

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Basic information

Entry
Database: PDB / ID: 2ast
TitleCrystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide
Components
  • (Cyclin-dependent ...) x 2
  • (S-phase kinase-associated protein ...) x 2
KeywordsLIGASE/LIGASE INHIBITOR / SCF-substrate complex / LRR / CELL CYCLE / PROTEIN TURNOVER COMPLEX / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / autophagic cell death / positive regulation of protein polyubiquitination / negative regulation of epithelial cell proliferation involved in prostate gland development / FOXO-mediated transcription of cell cycle genes / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects ...cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / autophagic cell death / positive regulation of protein polyubiquitination / negative regulation of epithelial cell proliferation involved in prostate gland development / FOXO-mediated transcription of cell cycle genes / F-box domain binding / Aberrant regulation of mitotic exit in cancer due to RB1 defects / PcG protein complex / regulation of cell cycle G1/S phase transition / regulation of exit from mitosis / epithelial cell proliferation involved in prostate gland development / negative regulation of phosphorylation / mitotic cell cycle phase transition / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / ubiquitin ligase activator activity / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus / cyclin-dependent protein serine/threonine kinase inhibitor activity / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / nuclear export / RHO GTPases activate CIT / cyclin-dependent protein serine/threonine kinase activator activity / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / AKT phosphorylates targets in the cytosol / Cul4A-RING E3 ubiquitin ligase complex / epithelial cell apoptotic process / SCF ubiquitin ligase complex / cellular response to antibiotic / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of kinase activity / ubiquitin ligase complex scaffold activity / molecular function inhibitor activity / protein kinase inhibitor activity / cellular response to lithium ion / p53-Dependent G1 DNA Damage Response / Prolactin receptor signaling / PTK6 Regulates Cell Cycle / protein monoubiquitination / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / Constitutive Signaling by AKT1 E17K in Cancer / cullin family protein binding / inner ear development / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of vascular associated smooth muscle cell proliferation / ubiquitin-like ligase-substrate adaptor activity / negative regulation of mitotic cell cycle / cellular response to organic cyclic compound / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / cyclin-dependent protein kinase holoenzyme complex / protein K48-linked ubiquitination / response to amino acid / localization / response to cadmium ion / response to glucose / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Nuclear events stimulated by ALK signaling in cancer / Cyclin E associated events during G1/S transition / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of microtubule polymerization / regulation of cell migration / Notch signaling pathway / Hsp70 protein binding / regulation of mitotic cell cycle / FLT3 Signaling / Regulation of BACH1 activity / cyclin binding / MAP3K8 (TPL2)-dependent MAPK1/3 activation / positive regulation of DNA replication / placenta development / ubiquitin 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 / sensory perception of sound / 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 / G1/S transition of mitotic cell cycle / 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 / 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 / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / negative regulation of cell growth / response to peptide hormone / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling
Similarity search - Function
Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. ...Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase inhibitor domain / Cyclin-dependent kinase inhibitor domain superfamily / Cyclin-dependent kinase inhibitor / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / 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 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / Cyclin-dependent kinase inhibitor 1B / Cyclin-dependent kinases regulatory subunit 1 / S-phase kinase-associated protein 1 / S-phase kinase-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHao, B. / Zhang, N. / Schulman, B.A. / Wu, G. / Pagano, M. / Pavletich, N.P.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural Basis of the Cks1-Dependent Recognition of p27(Kip1) by the SCF(Skp2) Ubiquitin Ligase.
Authors: Hao, B. / Zheng, N. / Schulman, B.A. / Wu, G. / Miller, J.J. / Pagano, M. / Pavletich, N.P.
History
DepositionAug 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: S-phase kinase-associated protein 1A
B: S-phase kinase-associated protein 2
C: Cyclin-dependent kinases regulatory subunit 1
D: Cyclin-dependent kinase inhibitor 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9086
Polymers65,6684
Non-polymers2402
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-33 kcal/mol
Surface area25720 Å2
MethodPISA
2
A: S-phase kinase-associated protein 1A
B: S-phase kinase-associated protein 2
C: Cyclin-dependent kinases regulatory subunit 1
D: Cyclin-dependent kinase inhibitor 1B
hetero molecules

A: S-phase kinase-associated protein 1A
B: S-phase kinase-associated protein 2
C: Cyclin-dependent kinases regulatory subunit 1
D: Cyclin-dependent kinase inhibitor 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,81612
Polymers131,3368
Non-polymers4814
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area13570 Å2
ΔGint-79 kcal/mol
Surface area50260 Å2
MethodPISA
3
A: S-phase kinase-associated protein 1A
B: S-phase kinase-associated protein 2
hetero molecules

A: S-phase kinase-associated protein 1A
B: S-phase kinase-associated protein 2
hetero molecules

C: Cyclin-dependent kinases regulatory subunit 1
D: Cyclin-dependent kinase inhibitor 1B
hetero molecules

C: Cyclin-dependent kinases regulatory subunit 1
D: Cyclin-dependent kinase inhibitor 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,81612
Polymers131,3368
Non-polymers4814
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
crystal symmetry operation3_545-x+y,-x-1,z+1/31
crystal symmetry operation5_545x-y,-y-1,-z+1/31
Buried area11460 Å2
ΔGint-63 kcal/mol
Surface area52370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.700, 148.700, 98.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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S-phase kinase-associated protein ... , 2 types, 2 molecules AB

#1: Protein S-phase kinase-associated protein 1A / Cyclin A/CDK2-associated protein p19 / p19A / p19skp1 / RNA polymerase II elongation factor-like ...Cyclin A/CDK2-associated protein p19 / p19A / p19skp1 / RNA polymerase II elongation factor-like protein / Organ of Corti protein 2 / OCP-II protein / OCP-2 / Transcription elongation factor B / SIII


Mass: 18135.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1A, EMC19, OCP2, SKP1, TCEB1L / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: Skp1 / References: UniProt: P63208
#2: Protein S-phase kinase-associated protein 2 / F-box protein Skp2 / Cyclin A/CDK2-associated protein p45 / p45skp2 / F-box/LRR-repeat protein 1


Mass: 37923.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP2, FBXL1 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: Skp2 / References: UniProt: Q13309

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Cyclin-dependent ... , 2 types, 2 molecules CD

#3: Protein Cyclin-dependent kinases regulatory subunit 1 / CKS-1


Mass: 8482.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKS1, CKS1B / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Keywords: Cks1 / References: UniProt: P61024
#4: Protein/peptide Cyclin-dependent kinase inhibitor 1B / Cyclin-dependent kinase inhibitor p27 / p27Kip1


Mass: 1126.154 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemical synthesis, this sequence occurs naturally in humans.
Keywords: p27 peptide / References: UniProt: P46527

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Non-polymers , 2 types, 267 molecules

#5: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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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: 4.9 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97946 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 8, 2005 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 55849 / Num. obs: 55849 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 35
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4 / Num. unique all: 5513 / Rsym value: 0.422 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FQV

1fqv


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.448 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22109 2826 5.1 %RANDOM
Rwork0.20178 ---
all0.2028 52996 --
obs0.2028 52996 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.844 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.25 Å20 Å2
2---0.49 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4377 0 18 265 4660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224483
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.9766074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1515540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74325.074203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90715815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9291521
X-RAY DIFFRACTIONr_chiral_restr0.0720.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023324
X-RAY DIFFRACTIONr_nbd_refined0.1890.22049
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2327
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.210
X-RAY DIFFRACTIONr_mcbond_it2.0081.82846
X-RAY DIFFRACTIONr_mcangle_it3.1234441
X-RAY DIFFRACTIONr_scbond_it2.762.51872
X-RAY DIFFRACTIONr_scangle_it4.18641633
LS refinement shellResolution: 2.303→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 195 -
Rwork0.285 3831 -
obs--100 %

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