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- EMDB-17152: AAA+ motor subunit ChlI of magnesium chelatase, hexamer conformation B -

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Basic information

Entry
Database: EMDB / ID: EMD-17152
TitleAAA+ motor subunit ChlI of magnesium chelatase, hexamer conformation B
Map data
Sample
  • Complex: ChlI in the presence of ATP
    • Protein or peptide: Magnesium-chelatase subunit ChlI
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsAAA+ / Magnesium Chelatase / Cyanobacteria / PHOTOSYNTHESIS
Function / homology
Function and homology information


magnesium chelatase / magnesium chelatase activity / chlorophyll biosynthetic process / photosynthesis / ATP hydrolysis activity / ATP binding
Similarity search - Function
Magnesium chelatase, ATPase subunit I / ChlI/MoxR, AAA lid domain / AAA lid domain / Magnesium-chelatase subunit ChlI-like / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Magnesium-chelatase subunit ChlI
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsShvarev D / Moeller A
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC 944 Germany
German Research Foundation (DFG)CRC1557 Germany
German Research Foundation (DFG)INST 190/196-1 FUGG Germany
German Federal Ministry for Education and ResearchJPND-DLR 01ED2010 Germany
CitationJournal: mBio / Year: 2023
Title: Conformational variability of cyanobacterial ChlI, the AAA+ motor of magnesium chelatase involved in chlorophyll biosynthesis.
Authors: Dmitry Shvarev / Alischa Ira Scholz / Arne Moeller /
Abstract: Photosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme ...Photosynthesis is an essential life process that relies on chlorophyll. In photosynthetic organisms, chlorophyll synthesis involves multiple steps and depends on magnesium chelatase. This enzyme complex is responsible for inserting magnesium into the chlorophyll precursor, but the molecular mechanism of this process is not fully understood. By using cryogenic electron microscopy and conducting functional analyses, we have discovered that the motor subunit ChlI of magnesium chelatase undergoes conformational changes in the presence of ATP. Our findings offer new insights into how energy is transferred from ChlI to the other components of magnesium chelatase. This information significantly contributes to our understanding of the initial step in chlorophyll biosynthesis and lays the foundation for future studies on the entire process of chlorophyll production.
History
DepositionApr 18, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17152.png

Downloads & links

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Map

FileDownload / File: emd_17152.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 288 pix.
= 266.112 Å		0.92 Å/pix.
x 288 pix.
= 266.112 Å		0.92 Å/pix.
x 288 pix.
= 266.112 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.924 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.3462829 - 0.6719823
Average (Standard dev.)0.0014147165 (±0.018563166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 266.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17152_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_17152_half_map_2.map
Projections & Slices
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Histogram

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Sample components

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Entire : ChlI in the presence of ATP

EntireName: ChlI in the presence of ATP
Components
  • Complex: ChlI in the presence of ATP
    • Protein or peptide: Magnesium-chelatase subunit ChlI
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: ChlI in the presence of ATP

SupramoleculeName: ChlI in the presence of ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)

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Macromolecule #1: Magnesium-chelatase subunit ChlI

MacromoleculeName: Magnesium-chelatase subunit ChlI / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: magnesium chelatase
Source (natural)Organism: Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Molecular weightTheoretical: 42.12593 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHTPT AQTTASARRV VFPFTAIVGQ EEMKLALLLN VIDPKIGGVM IMGDRGTGKS TTIRALADLL PEIPVVANDP FNSDPSDPD LMSDEVRQKS GTGAEIPIEF KKVQMVDLPL GATEDRVCGT IDIEKALSEG VKAFEPGLLA KANRGILYVD E VNLLDDHL ...String:
MHHHHHHTPT AQTTASARRV VFPFTAIVGQ EEMKLALLLN VIDPKIGGVM IMGDRGTGKS TTIRALADLL PEIPVVANDP FNSDPSDPD LMSDEVRQKS GTGAEIPIEF KKVQMVDLPL GATEDRVCGT IDIEKALSEG VKAFEPGLLA KANRGILYVD E VNLLDDHL VDVLLDSAAS GWNTVEREGI SIRHPARFVL VGSGNPEEGE LRPQLLDRFG MHAEIHTVKE PALRVQIVEQ RS EFDQNPP TFLEKYNPEQ TALQKKIVEA QKLLPEVKLD YDLRVKISEV CSELDVDGLR GDIVTNRAAK ALTAYEGRTE VTV DDIRRV ITLCLRHRLR KDPLESIDSG YKVEKVFARI FGVELLEDDS SQKNGAGQIK TGVR

UniProtKB: Magnesium-chelatase subunit ChlI

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80344
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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