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- EMDB-64229: CryoEM structure of Brucella melitensis CobS dodecamer 2 without ... -

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Basic information

Entry
Database: EMDB / ID: EMD-64229
TitleCryoEM structure of Brucella melitensis CobS dodecamer 2 without AMPPNP
Map data
Sample
  • Complex: CobS Dodecamer 2
    • Protein or peptide: Cobaltochelatase subunit CobS
KeywordsCobalt chelatase / CobS / AAA+ / ATPase / LIGASE
Function / homology
Function and homology information


cobaltochelatase / cobaltochelatase activity / cobalamin biosynthetic process / ATP hydrolysis activity / ATP binding
Similarity search - Function
Cobaltochelatase subunit CobS / Cobaltochelatase subunit CobS N-terminal domain / Cobaltochelatase CobS subunit N terminal / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cobaltochelatase subunit CobS
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.02 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_64229.png

Downloads & links

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Map

FileDownload / File: emd_64229.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: 0.01
Minimum - Maximum-0.001672185 - 2.1098125
Average (Standard dev.)0.0031667321 (±0.041020658)
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: #2

Fileemd_64229_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_64229_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 : CobS Dodecamer 2

EntireName: CobS Dodecamer 2
Components
  • Complex: CobS Dodecamer 2
    • Protein or peptide: Cobaltochelatase subunit CobS

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Supramolecule #1: CobS Dodecamer 2

SupramoleculeName: CobS Dodecamer 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Brucella melitensis (bacteria)

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Macromolecule #1: Cobaltochelatase subunit CobS

MacromoleculeName: Cobaltochelatase subunit CobS / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Brucella melitensis (bacteria)
Molecular weightTheoretical: 36.768629 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNKVERDIAN LPDTTVSVRE VFGIDSDMMV PAYAAGDSYV PELDPDYLFD RQTTLAILAG FAYNRRVMVS GYHGTGKSTH IEQVAARLN WPCVRVNLDS HVSRIDLVGK DAIVVKEGVQ VTEFKDGILP WAYQHNVALV FDEYDAGRPD VMFVIQRVLE S SGRLTLLD ...String:
MNKVERDIAN LPDTTVSVRE VFGIDSDMMV PAYAAGDSYV PELDPDYLFD RQTTLAILAG FAYNRRVMVS GYHGTGKSTH IEQVAARLN WPCVRVNLDS HVSRIDLVGK DAIVVKEGVQ VTEFKDGILP WAYQHNVALV FDEYDAGRPD VMFVIQRVLE S SGRLTLLD QSRVIRPHPA FRLFATANTV GLGDTTGLYH GTQQINQAQM DRWSIVTTLN YLPHDNEVNI VLVKAKHYQN AE GREIVNK MVRVADMTRQ AFINGDLSTV MSPRTVITWA ENAAIFNDVG FAFRLTFLNK CDELERATVA EFYQRAFGVE LPE SAANIV LA

UniProtKB: Cobaltochelatase subunit CobS

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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

Detailscryosparc
Particle selectionDetails: cryosparc
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135929
Initial angle assignmentType: OTHER
Final angle assignmentType: COMMON LINE

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