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- EMDB-3602: KaiCBA circadian clock backbone model based on a Cryo-EM density -

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Basic information

Entry
Database: EMDB / ID: EMD-3602
TitleKaiCBA circadian clock backbone model based on a Cryo-EM density
Map dataKaiCBA circadian clock complex
Sample
  • Complex: KaiCBA circadian clock complex
    • Protein or peptide: Circadian clock protein kinase KaiC
    • Protein or peptide: Circadian clock protein KaiB
    • Protein or peptide: Circadian clock protein KaiA
KeywordsAAA+-ATPase / Kinase / Circadian Clock Complex / Cyanobacteria / Fold-switch / Transferase
Function / homology
Function and homology information


detection of redox state / : / regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / negative regulation of phosphorylation / entrainment of circadian clock / positive regulation of circadian rhythm / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / regulation of circadian rhythm ...detection of redox state / : / regulation of phosphorelay signal transduction system / negative regulation of circadian rhythm / negative regulation of phosphorylation / entrainment of circadian clock / positive regulation of circadian rhythm / protein serine/threonine/tyrosine kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / regulation of circadian rhythm / circadian rhythm / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of DNA-templated transcription / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Circadian clock protein KaiA, N-terminal / Circadian clock protein KaiA, N-terminal domain / KaiA N-terminal domain profile. / Circadian clock protein KaiA / Circadian clock protein KaiB / Circadian clock protein KaiA, C-terminal / KaiA C-terminal domain / KaiA C-terminal domain profile. / KaiA / Circadian clock protein KaiB-like ...Circadian clock protein KaiA, N-terminal / Circadian clock protein KaiA, N-terminal domain / KaiA N-terminal domain profile. / Circadian clock protein KaiA / Circadian clock protein KaiB / Circadian clock protein KaiA, C-terminal / KaiA C-terminal domain / KaiA C-terminal domain profile. / KaiA / Circadian clock protein KaiB-like / KaiA/RbsU helical domain superfamily / KaiB domain / KaiB domain / KaiB / Circadian clock KaiC, bacteria / : / Circadian clock protein kinase KaiC / : / : / KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / CheY-like superfamily / Thioredoxin-like superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Circadian clock oscillator protein KaiC / Circadian clock oscillator protein KaiB / Circadian clock oscillator protein KaiA
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsSchuller JM / Snijder J
CitationJournal: Science / Year: 2017
Title: Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state.
Authors: Joost Snijder / Jan M Schuller / Anika Wiegard / Philip Lössl / Nicolas Schmelling / Ilka M Axmann / Jürgen M Plitzko / Friedrich Förster / Albert J R Heck /
Abstract: Cyanobacteria have a robust circadian oscillator, known as the Kai system. Reconstituted from the purified protein components KaiC, KaiB, and KaiA, it can tick autonomously in the presence of ...Cyanobacteria have a robust circadian oscillator, known as the Kai system. Reconstituted from the purified protein components KaiC, KaiB, and KaiA, it can tick autonomously in the presence of adenosine 5'-triphosphate (ATP). The KaiC hexamers enter a natural 24-hour reaction cycle of autophosphorylation and assembly with KaiB and KaiA in numerous diverse forms. We describe the preparation of stoichiometrically well-defined assemblies of KaiCB and KaiCBA, as monitored by native mass spectrometry, allowing for a structural characterization by single-particle cryo-electron microscopy and mass spectrometry. Our data reveal details of the interactions between the Kai proteins and provide a structural basis to understand periodic assembly of the protein oscillator.
History
DepositionFeb 24, 2017-
Header (metadata) releaseMar 29, 2017-
Map releaseMar 29, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0188
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0188
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5n8y
  • Surface level: 0.0188
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3602.png

Downloads & links

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Map

FileDownload / File: emd_3602.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKaiCBA circadian clock complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 196 pix.
= 264.6 Å		1.35 Å/pix.
x 196 pix.
= 264.6 Å		1.35 Å/pix.
x 196 pix.
= 264.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0188 / Movie #1: 0.0188
Minimum - Maximum-0.055518128 - 0.07684249
Average (Standard dev.)0.0001822975 (±0.0040218798)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 264.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z264.600264.600264.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.0560.0770.000

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Supplemental data

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Sample components

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Entire : KaiCBA circadian clock complex

EntireName: KaiCBA circadian clock complex
Components
  • Complex: KaiCBA circadian clock complex
    • Protein or peptide: Circadian clock protein kinase KaiC
    • Protein or peptide: Circadian clock protein KaiB
    • Protein or peptide: Circadian clock protein KaiA

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Supramolecule #1: KaiCBA circadian clock complex

SupramoleculeName: KaiCBA circadian clock complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechococcus elongatus (bacteria)

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Macromolecule #1: Circadian clock protein kinase KaiC

MacromoleculeName: Circadian clock protein kinase KaiC / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 58.072773 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSAEMTSPN NNSEHQAIAK MRTMIEGFDD ISHGGLPIGR STLVSGTSGT GKTLFSIQFL YNGIIEFDEP GVFVTFEETP QDIIKNARS FGWDLAKLVD EGKLFILDAS PDPEGQEVVG GFDLSALIER INYAIQKYRA RRVSIDSVTS VFQQYDASSV V RRELFRLV ...String:
MTSAEMTSPN NNSEHQAIAK MRTMIEGFDD ISHGGLPIGR STLVSGTSGT GKTLFSIQFL YNGIIEFDEP GVFVTFEETP QDIIKNARS FGWDLAKLVD EGKLFILDAS PDPEGQEVVG GFDLSALIER INYAIQKYRA RRVSIDSVTS VFQQYDASSV V RRELFRLV ARLKQIGATT VMTTERIEEY GPIARYGVEE FVSDNVVILR NVLEGERRRR TLEILKLRGT SHMKGEYPFT IT DHGINIF PLGAMRLTQR SSNVRVSSGV VRLDEMCGGG FFKDSIILAT GATGTGKTLL VSRFVENACA NKERAILFAY EES RAQLLR NAYSWGMDFE EMERQNLLKI VCAYPESAGL EDHLQIIKSE INDFKPARIA IDSLSALARG VSNNAFRQFV IGVT GYAKQ EEITGLFTNT SDQFMGAHSI TDSHISTITD TIILLQYVEI RGEMSRAINV FKMRGSWHDK AIREFMISDK GPDIK DSFR NFERIISGSP TRITVDEKSE LSRIVRGVQE KGPES

UniProtKB: Circadian clock oscillator protein KaiC

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Macromolecule #2: Circadian clock protein KaiB

MacromoleculeName: Circadian clock protein KaiB / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 11.450387 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSPRKTYILK LYVAGNTPNS VRALKTLKNI LEVEFQGVYA LKVIDVLKNP QLAEEDKILA TPTLAKVLPL PVRRIIGDLS DREKVLIGL DLLYGELQDS DDF

UniProtKB: Circadian clock oscillator protein KaiB

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Macromolecule #3: Circadian clock protein KaiA

MacromoleculeName: Circadian clock protein KaiA / type: protein_or_peptide / ID: 3 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus elongatus (bacteria)
Molecular weightTheoretical: 32.666199 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLSQIAICIW VESTAILQDC QRALSADRYQ LQVCESGEML LEYAQTHRDQ IDCLILVAAN PSFRAVVQQL CFEGVVVPAI VVGDRDSED PDEPAKEQLY HSAELHLGIH QLEQLPYQVD AALAEFLRLA PVETMADHIM LMGANHDPEL SSQQRDLAQR L QERLGYLG ...String:
MLSQIAICIW VESTAILQDC QRALSADRYQ LQVCESGEML LEYAQTHRDQ IDCLILVAAN PSFRAVVQQL CFEGVVVPAI VVGDRDSED PDEPAKEQLY HSAELHLGIH QLEQLPYQVD AALAEFLRLA PVETMADHIM LMGANHDPEL SSQQRDLAQR L QERLGYLG VYYKRDPDRF LRNLPAYESQ KLHQAMQTSY REIVLSYFSP NSNLNQSIDN FVNMAFFADV PVTKVVEIHM EL MDEFAKK LRVEGRSEDI LLDYRLTLID VIAHLCEMYR RSIPRET

UniProtKB: Circadian clock oscillator protein KaiA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridMaterial: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 15.2 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: 3D Shape with the approximate demensions of the 2D Classes
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32498
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-5n8y:
KaiCBA circadian clock backbone model based on a Cryo-EM density

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