9OFH | pdb_00009ofh

Extended conformation of dusk state KaiC

PDB DOI: https://doi.org/10.2210/pdb9OFH/pdb
EM Map EMD-70432: EMDB EMDataResource

Classification: CIRCADIAN CLOCK PROTEIN
Organism(s): Synechococcus elongatus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-29 Released: 2025-05-14
Deposition Author(s): Dzimianski, J.V., Crosby, P., Balasco Serrao, V.H., Partch, C.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Extended conformation of dusk state KaiC

Dzimianski, J.V., Crosby, P., Balasco Serrao, V.H., Partch, C.L.

To be published.

Macromolecule Content

Total Structure Weight: 361.22 kDa
Atom Count: 22,356
Modeled Residue Count: 2,778
Deposited Residue Count: 3,162
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Circadian clock oscillator protein KaiC	A, B, C, D, E A, B, C, D, E, F	527	Synechococcus elongatus	Mutation(s): 0 Gene Names: kaiC, Synpcc7942_1216, see0011 EC: 2.7.11.1 (PDB Primary Data), 3.6.4 (PDB Primary Data)
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q79PF4
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot	0.9.8.95
MODEL REFINEMENT	ISOLDE	1.8
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4.4.1

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM141849
Howard Hughes Medical Institute (HHMI)	United States	--