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- EMDB-64246: CryoEM structure of Brucella melitensis CobS dodecamer 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-64246
TitleCryoEM structure of Brucella melitensis CobS dodecamer 1
Map data
Sample
  • Complex: apoCobS Dodecamer 1
    • Protein or peptide: CobS
KeywordsCobalt chelatase / CobS / AAA+ / ATPase / LIGASE
Biological speciesBrucella melitensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.62 Å
AuthorsZhou YL / Chen X / Liu L
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471323 China
National Natural Science Foundation of China (NSFC)32371270 China
CitationJournal: Biorxiv / Year: 2026
Title: Assembly of the ATP-driven cobalt chelatase
Authors: Zhou YL / Yuan H / Wu YC / Wang J / Chen H / Yao L / Wang M / Wang X / Wang J / He C / Chen X / Liu L
History
DepositionApr 17, 2025-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64246.png

Downloads & links

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Map

FileDownload / File: emd_64246.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.7 Å/pix.
x 400 pix.
= 279.2 Å		0.7 Å/pix.
x 400 pix.
= 279.2 Å		0.7 Å/pix.
x 400 pix.
= 279.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.698 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.011599242 - 0.06987548
Average (Standard dev.)0.0007112566 (±0.0066054757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 279.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64246_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64246_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : apoCobS Dodecamer 1

EntireName: apoCobS Dodecamer 1
Components
  • Complex: apoCobS Dodecamer 1
    • Protein or peptide: CobS

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Supramolecule #1: apoCobS Dodecamer 1

SupramoleculeName: apoCobS Dodecamer 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Brucella melitensis (bacteria)

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Macromolecule #1: CobS

MacromoleculeName: CobS / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Brucella melitensis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKVERDIAN LPDTTVSVRE VFGIDSDMMV PAYAAGDSYV PELDPDYLFD RQTTLAILAG FAYNRRVMVS GYHGTGKSTH IEQVAARLNW PCVRVNLDSH VSRIDLVGKD AIVVKEGVQV TEFKDGILPW AYQHNVALVF DEYDAGRPDV MFVIQRVLES SGRLTLLDQS ...String:
MNKVERDIAN LPDTTVSVRE VFGIDSDMMV PAYAAGDSYV PELDPDYLFD RQTTLAILAG FAYNRRVMVS GYHGTGKSTH IEQVAARLNW PCVRVNLDSH VSRIDLVGKD AIVVKEGVQV TEFKDGILPW AYQHNVALVF DEYDAGRPDV MFVIQRVLES SGRLTLLDQS RVIRPHPAFR LFATANTVGL GDTTGLYHGT QQINQAQMDR WSIVTTLNYL PHDNEVNIVL VKAKHYQNAE GREIVNKMVR VADMTRQAFI NGDLSTVMSP RTVITWAENA AIFNDVGFAF RLTFLNKCDE LERATVAEFY QRAFGVELPE SAANIVLA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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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: 2.0 µm / Nominal defocus min: 0.4 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20162
Initial angle assignmentType: OTHER
Final angle assignmentType: COMMON LINE

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