5C5E | pdb_00005c5e

Structure of KaiA dimer in complex with C-terminal KaiC peptide at 2.8 A resolution

PDB DOI: https://doi.org/10.2210/pdb5C5E/pdb

Classification: TRANSCRIPTION
Organism(s): Synechococcus elongatus PCC 7942 = FACHB-805, synthetic construct
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2015-06-19 Released: 2015-08-05
Deposition Author(s): Pattanayek, R., Egli, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.303 (Depositor), 0.295 (DCC)
R-Value Work:
0.240 (Depositor), 0.252 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Protein-Protein Interactions in the Cyanobacterial Circadian Clock: Structure of KaiA Dimer in Complex with C-Terminal KaiC Peptides at 2.8 angstrom Resolution.

Pattanayek, R., Egli, M.

(2015) Biochemistry 54: 4575-4578

PubMed: 26200123 Search on PubMed
DOI: https://doi.org/10.1021/acs.biochem.5b00694
Primary Citation Related Structures:
5C5E

PubMed Abstract:
In the cyanobacterial circadian clock, the KaiA, -B, and -C proteins with ATP constitute a post-translational oscillator. KaiA stimulates the KaiC autokinase, and KaiB antagonizes KaiA action. KaiA contacts the intrinsically disordered C-terminal regions of KaiC hexamer to promote phosphorylation across subunit interfaces. The crystal structure of KaiA dimer from Synechococcus elongatus with two KaiC C-terminal 20mer peptides bound reveals that the latter adopt an α-helical conformation and contact KaiA α-helical bundles via mostly hydrophobic interactions. This complex and the crystal structure of KaiC hexamer with truncated C-terminal tails can be fit into the electron microscopy (EM) density of the KaiA:KaiC complex. The hybrid model helps rationalize clock phenotypes of KaiA and KaiC mutants.

Organizational Affiliation

Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States.

Macromolecule Content

Total Structure Weight: 72.3 kDa
Atom Count: 5,018
Modeled Residue Count: 604
Deposited Residue Count: 620
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Circadian clock protein KaiA	A, C [auth B]	290	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0 Gene Names: kaiA, Synpcc7942_1218, see0009
UniProt
Find proteins for Q79PF6 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q79PF6 Go to UniProtKB: Q79PF6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q79PF6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KaiC C-terminal peptide	B [auth G], D [auth H]	20	synthetic construct	Mutation(s): 0 EC: 3.6.4 (UniProt), 2.7.11.1 (UniProt)
UniProt
Find proteins for Q79PF4 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q79PF4 Go to UniProtKB: Q79PF4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q79PF4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
52M Query on 52M Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(sulfanylcarbonyl)amino]benzoic acid C₂₁ H₁₃ N O₆ S YMGUTVDFHHFZIJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.303 (Depositor), 0.295 (DCC)
R-Value Work: 0.240 (Depositor), 0.252 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.43	α = 90
b = 97.43	β = 90
c = 124.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PHASER	phasing
Coot	model building
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Pattanayek, R.

Egli, M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM073845

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2015-08-12
Changes: Database references
Version 1.2: 2017-09-27
Changes: Author supporting evidence, Database references, Derived calculations
Version 1.3: 2019-12-25
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description