[English] 日本語
Yorodumi
- PDB-8bya: Cryo-EM structure of SKP1-SKP2-CKS1-CDK2-CyclinA-p27KIP1 Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bya
TitleCryo-EM structure of SKP1-SKP2-CKS1-CDK2-CyclinA-p27KIP1 Complex
Components
  • (Cyclin-dependent kinase ...) x 2
  • (S-phase kinase-associated protein ...) x 2
  • Cyclin-A2
  • Cyclin-dependent kinases regulatory subunit 1
  • p27 KIP1 C-terminus
KeywordsCELL CYCLE / cyclin-dependent kinase / signalling / ubiquitination
Function / homology
Function and homology information


negative regulation of growth / regulation of xenophagy / cyclin A2-CDK1 complex / F-box domain binding / synaptic assembly at neuromuscular junction / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of cell cycle process / neural crest cell differentiation / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus ...negative regulation of growth / regulation of xenophagy / cyclin A2-CDK1 complex / F-box domain binding / synaptic assembly at neuromuscular junction / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of cell cycle process / neural crest cell differentiation / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / G2/M DNA replication checkpoint / regulation of BMP signaling pathway / PcG protein complex / programmed cell death / cyclin-dependent protein serine/threonine kinase inhibitor activity / regulation of mitophagy / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / regulation of centrosome duplication / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / male pronucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cellular response to cocaine / female pronucleus / regulation of TOR signaling / response to glucagon / cyclin-dependent protein serine/threonine kinase activator activity / ubiquitin ligase activator activity / regulation of DNA damage checkpoint / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA biosynthetic process / SCF ubiquitin ligase complex / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to insulin-like growth factor stimulus / cyclin A2-CDK2 complex / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity / regulation of heterochromatin organization / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / regulation of mitotic cell cycle phase transition / X chromosome / PTK6 Regulates Cell Cycle / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Prolactin receptor signaling / regulation of anaphase-promoting complex-dependent catabolic process / limb development / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / ubiquitin ligase complex scaffold activity / regulation of DNA replication / animal organ regeneration / microtubule organizing center / G0 and Early G1 / cochlea development / centrosome duplication / Telomere Extension By Telomerase / Activation of the pre-replicative complex / cilium assembly / cullin family protein binding / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Activation of ATR in response to replication stress / protein K63-linked ubiquitination / Cyclin E associated events during G1/S transition / cyclin-dependent protein kinase holoenzyme complex / cellular response to platelet-derived growth factor stimulus / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of double-strand break repair via homologous recombination / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin A/B1/B2 associated events during G2/M transition / ubiquitin-like ligase-substrate adaptor activity / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / Nuclear events stimulated by ALK signaling in cancer / cellular response to nitric oxide / protein K48-linked ubiquitination / negative regulation of protein localization to chromatin / post-translational protein modification / regulation of mitotic cell cycle / cyclin binding / positive regulation of DNA replication / molecular function activator activity / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / peptidyl-serine phosphorylation / cellular response to estradiol stimulus / ubiquitin binding / G1/S transition of mitotic cell cycle
Similarity search - Function
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 ...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. / Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / 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 / Cyclin, N-terminal / Cyclin, N-terminal domain / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / SKP1/BTB/POZ domain superfamily / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Cyclin-dependent kinase inhibitor 1B / Cyclin-A2 / Cyclin-dependent kinase 2 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsRowland, R.J. / Salamina, M. / Endicott, J.A. / Noble, M.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N009738/1 and MR/V029142/1 United Kingdom
CitationJournal: Sci Rep / Year: 2023
Title: Cryo-EM structure of SKP1-SKP2-CKS1 in complex with CDK2-cyclin A-p27KIP1.
Authors: Rhianna J Rowland / Richard Heath / Daniel Maskell / Rebecca F Thompson / Neil A Ranson / James N Blaza / Jane A Endicott / Martin E M Noble / Marco Salamina /
Abstract: p27KIP1 (cyclin-dependent kinase inhibitor 1B, p27) is a member of the CIP/KIP family of CDK (cyclin dependent kinase) regulators that inhibit cell cycle CDKs. p27 phosphorylation by CDK1/2, signals ...p27KIP1 (cyclin-dependent kinase inhibitor 1B, p27) is a member of the CIP/KIP family of CDK (cyclin dependent kinase) regulators that inhibit cell cycle CDKs. p27 phosphorylation by CDK1/2, signals its recruitment to the SCF (S-phase kinase associated protein 1 (SKP1)-cullin-SKP2) E3 ubiquitin ligase complex for proteasomal degradation. The nature of p27 binding to SKP2 and CKS1 was revealed by the SKP1-SKP2-CKS1-p27 phosphopeptide crystal structure. Subsequently, a model for the hexameric CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex was proposed by overlaying an independently determined CDK2-cyclin A-p27 structure. Here we describe the experimentally determined structure of the isolated CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex at 3.4 Å global resolution using cryogenic electron microscopy. This structure supports previous analysis in which p27 was found to be structurally dynamic, transitioning from disordered to nascent secondary structure on target binding. We employed 3D variability analysis to further explore the conformational space of the hexameric complex and uncovered a previously unidentified hinge motion centred on CKS1. This flexibility gives rise to open and closed conformations of the hexameric complex that we propose may contribute to p27 regulation by facilitating recognition with SCF. This 3D variability analysis further informed particle subtraction and local refinement approaches to enhance the local resolution of the complex.
History
DepositionDec 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: Cyclin-A2
C: Cyclin-dependent kinase inhibitor 1B
D: S-phase kinase-associated protein 1
E: S-phase kinase-associated protein 2
F: Cyclin-dependent kinases regulatory subunit 1
G: p27 KIP1 C-terminus


Theoretical massNumber of molelcules
Total (without water)177,5867
Polymers177,5867
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, single peak
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Cyclin-dependent kinase ... , 2 types, 2 molecules AC

#1: Protein Cyclin-dependent kinase 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 33994.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Thr160 phosphorylated CDK2 / Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLySs / References: UniProt: P24941, cyclin-dependent kinase
#3: Protein Cyclin-dependent kinase inhibitor 1B / Cyclin-dependent kinase inhibitor p27 / p27Kip1


Mass: 17678.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: p27 kip1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYSs / References: UniProt: O43806

-
Protein , 2 types, 2 molecules BF

#2: Protein Cyclin-A2 / Cyclin-A / Cyclin A


Mass: 48609.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNA2, CCN1, CCNA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYSs / References: UniProt: P20248
#6: Protein Cyclin-dependent kinases regulatory subunit 1 / CKS-1


Mass: 9679.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKS1B, CKS1, PNAS-143, PNAS-16 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYSs / References: UniProt: P61024

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

#4: 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: 18679.965 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYSs / References: UniProt: P63208
#5: Protein S-phase kinase-associated protein 2 / Cyclin-A/CDK2-associated protein p45 / F-box protein Skp2 / F-box/LRR-repeat protein 1 / p45skp2


Mass: 47817.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP2, FBXL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYSs / References: UniProt: Q13309

-
Protein/peptide , 1 types, 1 molecules G

#7: Protein/peptide p27 KIP1 C-terminus


Mass: 1126.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminus of p27 KIP1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLYSs

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Hexameric complex of SKP1-SKP2-CKS1 with CDK2-CyclinA-p27(kip1)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.175 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3)pLYSs
Buffer solutionpH: 7.8
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 9 sec. / Electron dose: 65 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameCategoryDetails (eV)
1cryoSPARCparticle selectionblob picker
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignmenthomogeneous refinement
11cryoSPARCfinal Euler assignmentnon-uniform refinement
12cryoSPARCclassificationheterogenous refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1110356
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136325 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 121 / Protocol: RIGID BODY FIT / Space: REAL
Details: Initial fitting was performed in chimera followed by real space refinement in Phenix
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058609
ELECTRON MICROSCOPYf_angle_d0.69811782
ELECTRON MICROSCOPYf_dihedral_angle_d5.411210
ELECTRON MICROSCOPYf_chiral_restr0.0421395
ELECTRON MICROSCOPYf_plane_restr0.0061509

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more