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- PDB-2ass: Crystal structure of the Skp1-Skp2-Cks1 complex -

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Basic information

Entry
Database: PDB / ID: 2ass
TitleCrystal structure of the Skp1-Skp2-Cks1 complex
Components
  • (S-phase kinase-associated protein ...) x 2
  • Cyclin-dependent kinases regulatory subunit 1
KeywordsCELL CYCLE/LIGASE/PROTEIN TURNOVER / protein-protein complex / LRR / SCF / CELL CYCLE-LIGASE-PROTEIN TURNOVER COMPLEX
Function / homology
Function and homology information


synaptic assembly at neuromuscular junction / Aberrant regulation of mitotic exit in cancer due to RB1 defects / F-box domain binding / PcG protein complex / regulation of xenophagy / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul7-RING ubiquitin ligase complex / cyclin-dependent protein serine/threonine kinase activator activity / regulation of cell cycle process ...synaptic assembly at neuromuscular junction / Aberrant regulation of mitotic exit in cancer due to RB1 defects / F-box domain binding / PcG protein complex / regulation of xenophagy / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / Cul7-RING ubiquitin ligase complex / cyclin-dependent protein serine/threonine kinase activator activity / regulation of cell cycle process / neural crest cell differentiation / regulation of BMP signaling pathway / ubiquitin ligase activator activity / regulation of mitophagy / regulation of centrosome duplication / regulation of TOR signaling / SCF ubiquitin ligase complex / regulation of DNA damage checkpoint / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / ubiquitin ligase complex scaffold activity / limb development / cyclin-dependent protein kinase holoenzyme complex / cullin family protein binding / centrosome duplication / protein K63-linked ubiquitination / cilium assembly / positive regulation of double-strand break repair via homologous recombination / ubiquitin-like ligase-substrate adaptor activity / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / molecular function activator activity / regulation of mitotic cell cycle / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / G1/S transition of mitotic cell cycle / ubiquitin binding / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Activation of NF-kappaB in B cells / Iron uptake and transport / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / beta-catenin binding / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / NOTCH1 Intracellular Domain Regulates Transcription / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / protein polyubiquitination / Interleukin-1 signaling / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Orc1 removal from chromatin / Cyclin D associated events in G1 / Regulation of RUNX2 expression and activity / Regulation of PLK1 Activity at G2/M Transition / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / regulation of inflammatory response / Neddylation / heterochromatin formation / histone binding / defense response to virus / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / intracellular iron ion homeostasis / regulation of cell cycle / protein ubiquitination / Ub-specific processing proteases / chromatin remodeling / protein domain specific binding / innate immune response / cell division / negative regulation of DNA-templated transcription / centrosome / nucleolus / regulation of DNA-templated transcription / protein kinase binding / chromatin / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / 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 ...Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / 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 / 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 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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 / Leucine-rich repeat domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / PHOSPHATE ION / 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: 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: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_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

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0678
Polymers64,5423
Non-polymers5255
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-47 kcal/mol
Surface area24900 Å2
MethodPISA
2
A: S-phase kinase-associated protein 1A
B: S-phase kinase-associated protein 2
C: Cyclin-dependent kinases regulatory subunit 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)130,13416
Polymers129,0836
Non-polymers1,05010
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area13010 Å2
ΔGint-107 kcal/mol
Surface area48670 Å2
MethodPISA
3
C: Cyclin-dependent kinases regulatory subunit 1
hetero molecules

C: Cyclin-dependent kinases regulatory subunit 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)130,13416
Polymers129,0836
Non-polymers1,05010
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_545-x+y,-x-1,z+1/31
crystal symmetry operation5_545x-y,-y-1,-z+1/31
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area11160 Å2
ΔGint-94 kcal/mol
Surface area50510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.332, 149.332, 99.916
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 / Mutation: P1A
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) / 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) / References: UniProt: Q13309

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Protein , 1 types, 1 molecules C

#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) / References: UniProt: P61024

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Non-polymers , 3 types, 72 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-BEN / BENZAMIDINE


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


Mass: 18.015 Da / Num. of mol.: 67 / 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: 7.6
Details: BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1.04187 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 26, 2004 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04187 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 25854 / Num. obs: 25854 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 10
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2548 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FQV

1fqv


Resolution: 3→19.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 277074.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1960 7.9 %RANDOM
Rwork0.214 ---
all0.214 25977 --
obs0.214 24867 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.2007 Å2 / ksol: 0.271649 e/Å3
Displacement parametersBiso mean: 61.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.32 Å29.9 Å20 Å2
2---6.08 Å20 Å2
3---11.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 33 67 4404
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 321 8.2 %
Rwork0.326 3592 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3bam.param
X-RAY DIFFRACTION4ion.param

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