SAXSdb — 5n8y

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Circadian clock protein kinase KaiC

Synechococcus elongatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Circadian clock protein KaiB × 6 （Q79PF5） Circadian clock protein KaiA × 12 （Q79PF6）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAIC_SYNE7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–519； UniProt 1–519 Author chain B； PDBConstruct 1–519； UniProt 1–519 Author chain C； PDBConstruct 1–519； UniProt 1–519 Author chain D； PDBConstruct 1–519； UniProt 1–519 Author chain E； PDBConstruct 1–519； UniProt 1–519 Author chain F； PDBConstruct 1–519； UniProt 1–519

Circadian clock protein KaiB

Synechococcus elongatus

UniProt Q79PF5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Circadian clock protein kinase KaiC × 6 （Q79PF4） Circadian clock protein KaiA × 12 （Q79PF6）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAIB_SYNE7
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–102； UniProt 1–102 Author chain H； PDBConstruct 1–102； UniProt 1–102 Author chain I； PDBConstruct 1–102； UniProt 1–102 Author chain J； PDBConstruct 1–102； UniProt 1–102 Author chain K； PDBConstruct 1–102； UniProt 1–102 Author chain L； PDBConstruct 1–102； UniProt 1–102

Circadian clock protein KaiA

Synechococcus elongatus

UniProt Q79PF6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Circadian clock protein kinase KaiC × 6 （Q79PF4） Circadian clock protein KaiB × 6 （Q79PF5）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KAIA_SYNE7
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain M； PDBConstruct 1–284； UniProt 1–284 Author chain N； PDBConstruct 1–284； UniProt 1–284 Author chain O； PDBConstruct 1–284； UniProt 1–284 Author chain P； PDBConstruct 1–284； UniProt 1–284 Author chain Q； PDBConstruct 1–284； UniProt 1–284 Author chain R； PDBConstruct 1–284； UniProt 1–284 Author chain S； PDBConstruct 1–284； UniProt 1–284 Author chain T； PDBConstruct 1–284； UniProt 1–284 Author chain U； PDBConstruct 1–284； UniProt 1–284 Author chain V； PDBConstruct 1–284； UniProt 1–284 Author chain W； PDBConstruct 1–284； UniProt 1–284 Author chain X； PDBConstruct 1–284； UniProt 1–284

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5n8y
Deposition date deposition_date	2017-02-24
Structure title title	KaiCBA circadian clock backbone model based on a Cryo-EM density
Keywords keywords	AAA+-ATPase, Kinase, Circadian Clock Complex, Cyanobacteria, Fold-switch, Transferase; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5n8y__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5n8y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5n8y__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	55.81 Å
Rg (electron density)	55.45 Å
Total Rg	55.65 Å
Atom count	23514
Residues	4752
Excluded volume	378730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5n8y__assembly_1__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Circadian clock protein kinase KaiC
Molecular weight formula_weight	58072.8 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	23514

MTSAEMTSPNNNSEHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLTQRSSNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGLFTNTSDQFMGAHSITDSHISTITDTIILLQYVEIRGEMSRAINVFKMRGSWHDKAIREFMISDKGPDIKDSFRNFERIISGSPTRITVDEKSELSRIVRGVQEKGPES

Source Source

Source organism organism	Synechococcus elongatus
NCBI taxonomy ID ncbi_taxonomy_id	32046
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Circadian clock protein KaiB
Molecular weight formula_weight	11450.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,K,J,I,L

MSPRKTYILKLYVAGNTPNSVRALKTLKNILEVEFQGVYALKVIDVLKNPQLAEEDKILATPTLAKVLPLPVRRIIGDLSDREKVLIGLDLLYGELQDSDDF

Source Source

Source organism organism	Synechococcus elongatus
NCBI taxonomy ID ncbi_taxonomy_id	32046
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Circadian clock protein KaiA
Molecular weight formula_weight	32666.2 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O,P,Q,R,S,T,U,V,W,X

MLSQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQTHRDQIDCLILVAANPSFRAVVQQLCFEGVVVPAIVVGDRDSEDPDEPAKEQLYHSAELHLGIHQLEQLPYQVDAALAEFLRLAPVETMADHIMLMGANHDPELSSQQRDLAQRLQERLGYLGVYYKRDPDRFLRNLPAYESQKLHQAMQTSYREIVLSYFSPNSNLNQSIDNFVNMAFFADVPVTKVVEIHMELMDEFAKKLRVEGRSEDILLDYRLTLIDVIAHLCEMYRRSIPRET

Source Source

Source organism organism	Synechococcus elongatus
NCBI taxonomy ID ncbi_taxonomy_id	32046
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.70 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	32498

KaiCBA circadian clock backbone model based on a Cryo-EM density

1. Protein Identity and Related Structures Protein Identity & Related Structures

Circadian clock protein kinase KaiC

State in the Current Structure

Other States of the Same Protein in the Database

Circadian clock protein KaiB

State in the Current Structure

Other States of the Same Protein in the Database

Circadian clock protein KaiA

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5n8y__assembly_1__model_1

5n8y__assembly_1__model_1 | I(q)

5n8y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)

KaiCBA circadian clock backbone model based on a Cryo-EM density

1. Protein Identity and Related Structures Protein Identity & Related Structures

Circadian clock protein kinase KaiC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Circadian clock protein KaiB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Circadian clock protein KaiA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5n8y__assembly_1__model_1

5n8y__assembly_1__model_1 | I(q)

5n8y__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

7. Citations (1)