4LPA

Crystal structure of a Cdc6 phosphopeptide in complex with Cks1

PDB DOI: https://doi.org/10.2210/pdb4LPA/pdb

Classification: PROTEIN BINDING
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-07-15 Released: 2013-11-06
Deposition Author(s): McGrath, D.A., Balog, E.R.M., Koivomagi, M., Lucena, R., Mai, M.V., Hirschi, A., Kellogg, D.R., Loog, M., Rubin, S.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.281
R-Value Work: 0.245
R-Value Observed: 0.248

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Cks confers specificity to phosphorylation-dependent CDK signaling pathways.

McGrath, D.A., Balog, E.R., Koivomagi, M., Lucena, R., Mai, M.V., Hirschi, A., Kellogg, D.R., Loog, M., Rubin, S.M.

(2013) Nat Struct Mol Biol 20: 1407-1414

PubMed: 24186063 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nsmb.2707
Primary Citation of Related Structures:
4LPA

PubMed Abstract:
Cks is an evolutionarily conserved protein that regulates cyclin-dependent kinase (CDK) activity. Clarifying the underlying mechanisms and cellular contexts of Cks function is critical because Cks is essential for proper cell growth, and its overexpression has been linked to cancer. We observe that budding-yeast Cks associates with select phosphorylated sequences in cell cycle-regulatory proteins. We characterize the molecular interactions responsible for this specificity and demonstrate that Cks enhances CDK activity in response to specific priming phosphosites. Identification of the binding consensus sequence allows us to identify putative Cks-directed CDK substrates and binding partners. We characterize new Cks-binding sites in the mitotic regulator Wee1 and discover a new role for Cks in regulating CDK activity at mitotic entry. Together, our results portray Cks as a multifunctional phosphoadaptor that serves as a specificity factor for CDK activity.

Organizational Affiliation

1] Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California, USA. [2].

Macromolecule Content

Total Structure Weight: 57.05 kDa
Atom Count: 3,852
Modelled Residue Count: 452
Deposited Residue Count: 476
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinases regulatory subunit	A, B, C, D	119	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: CKS1, YBR1011, YBR135W
UniProt
Find proteins for P20486 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20486 Go to UniProtKB: P20486
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20486
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	A, B, C, D	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.281
R-Value Work: 0.245
R-Value Observed: 0.248
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.69	α = 90
b = 84.69	β = 90
c = 239.93	γ = 90

Software Package:

Software Name	Purpose
JBluIce-EPICS	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALEIT	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-11-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-06
Type: Initial release
Version 1.1: 2014-02-05
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description