Macromolecule Content

Total Structure Weight: 354.73 kDa
Atom Count: 22049
Modelled Residue Count: 2760
Deposited Residue Count: 3114
Unique protein chains: 1

7S65

Compressed conformation of nighttime state KaiC

PDB DOI: 10.2210/pdb7S65/pdb
EM Map EMD-24850: EMDB EMDataResource

Classification: CIRCADIAN CLOCK PROTEIN
Organism(s): Synechococcus elongatus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2021-09-13 Released: 2021-09-22
Deposition Author(s): Sandate, C.R., Swan, J.A., Partch, C.L., Lander, G.C.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Hidden conformations differentiate day and night in a circadian pacemaker

Swan, J.A., Sandate, C.R., Chavan, A.G., Freeberg, A.M., Etwaru, D., Palacios, J.G., Golden, S.S., Liwang, A., Lander, G.C., Partch, C.L.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Circadian clock protein kinase KaiC	A, B, C, D, E, F A, B, C, D, E, F	519	Synechococcus elongatus	Mutation(s): 2 Gene Names: kaiC, Synpcc7942_1216, see0011 EC: 2.7.11.1
UniProt
Find proteins for Q79PF4 (Synechococcus elongatus (strain PCC 7942 / FACHB-805)) Explore Q79PF4 Go to UniProtKB: Q79PF4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q79PF4
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E]	BA [auth F], CA [auth F], I [auth A], L [auth B], M [auth B], BA [auth F], CA [auth F], I [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], U [auth D], X [auth E], Y [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Ligand Interaction
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain T [auth D] MOL2 format, chain H [auth A] MOL2 format, chain T [auth D]	H [auth A], T [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Ligand Interaction
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth F] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain R [auth C] SDF format, chain S [auth D] SDF format, chain V [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth E]	AA [auth F], DA [auth F], G [auth A], J [auth A], K [auth B], AA [auth F], DA [auth F], G [auth A], J [auth A], K [auth B], N [auth B], O [auth C], R [auth C], S [auth D], V [auth D], W [auth E], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2021-09-13
Released Date: 2021-09-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	R21GM142196

Revision History (Full details and data files)

Version 1.0: 2021-09-22
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.