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- EMDB-64231: CryoEM structure of Brucella melitensis CobN with cobalt ion -

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Basic information

Entry
Database: EMDB / ID: EMD-64231
TitleCryoEM structure of Brucella melitensis CobN with cobalt ion
Map data
Sample
  • Complex: CobN
    • Protein or peptide: Cobaltochelatase subunit CobN
  • Ligand: COBALT (II) ION
KeywordsCobalt chelatase / CobN / Cobalt ion / LIGASE
Function / homologyCobaltochelatase, CobN subunit / CobN/magnesium chelatase / CobN/Magnesium Chelatase / cobaltochelatase / cobaltochelatase activity / cobalamin biosynthetic process / Cobaltochelatase subunit CobN
Function and homology information
Biological speciesBrucella melitensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 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_64231.png

Downloads & links

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Map

FileDownload / File: emd_64231.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 223.36 Å		0.7 Å/pix.
x 320 pix.
= 223.36 Å		0.7 Å/pix.
x 320 pix.
= 223.36 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: 0.03
Minimum - Maximum-0.0016442785 - 2.1441622
Average (Standard dev.)0.0017074217 (±0.031393267)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 223.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64231_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_64231_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 : CobN

EntireName: CobN
Components
  • Complex: CobN
    • Protein or peptide: Cobaltochelatase subunit CobN
  • Ligand: COBALT (II) ION

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Supramolecule #1: CobN

SupramoleculeName: CobN / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Brucella melitensis (bacteria)

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Macromolecule #1: Cobaltochelatase subunit CobN

MacromoleculeName: Cobaltochelatase subunit CobN / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Brucella melitensis (bacteria)
Molecular weightTheoretical: 136.922812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHLLLAQKGT ISDGNEAVDL GQTPGEIVFL SAADTELASI AQAHRLAPDM PSLRLANFLG LTHPMSVDAY VERTARHAKL IVVRIIGGE TYWPYGLEAL HACAITHGAK MAVLPGDDKP DHGLDRFSTI PAGERDDLWH YLIESGAANT HGFLAYCKAL I SGCEKPEA ...String:
MHLLLAQKGT ISDGNEAVDL GQTPGEIVFL SAADTELASI AQAHRLAPDM PSLRLANFLG LTHPMSVDAY VERTARHAKL IVVRIIGGE TYWPYGLEAL HACAITHGAK MAVLPGDDKP DHGLDRFSTI PAGERDDLWH YLIESGAANT HGFLAYCKAL I SGCEKPEA AAPLLKAGLW WPGEAVSSLT SVQRHWADPA APVAAIILYR ALVQSGQTQP VDALIAALQA RGLNPLPIFV SS LKDPLSA AVVDGLFEDC PPDIVLNATG FAISSPGAER KPTVLDKRGN MVLQVIFSGT PKTVWEASQQ GLLARDLAMN VAL PEVDGR VLSRAVSFKS AQQFDASVEA NIVTHEPHPD RVAFVAELAA NWVRLKRKPP AERRVALILA NYPNRDGRLG NGVG LDTPA GTVEVLRAMA AEGYRVGEIP ADSDALMRAL MAGPTNAARD GREIRETISL NQYKALFGKL ALTIQAEVEA RWGAP ENDP YFARELDAFA LPLMRFGETF VGIQPARGYN IDPKETYHSL DLVPPHGYIA YYAYLRAVAG VDAVVHMGKH GNLEWL PGK ALALSQNCYP EAVFGPMPHI YPFIVNDPGE GTQAKRRASA VIIDHLTPPL TRAESYGPLK DLEALVDEYY EASGVDP RR LLRLKAQILD LVRDIGLDRD AGIHDHDDED MALQKLDAYL CDLKEMQIRD GLHVFGLAPQ ARLLTDLLVA LARVPRGI P VSLGGAPGDQ SLQRAIAADA GLGEGFDPLD CNMAEPWAGA KPDMLLAASP ATWRIAGDTV ERIEILAAQL VAGEVPCPE DWTQTRAVLQ SIEEQLRPMV VSCGPSEIDG FLAALSGRFV PPGPSGAPTR GRPDVLPTGR NFFSTDSRAV PTPAAWELGK KSAELLITR YTQDHGEWPT SFGLTAWGTS NMRTGGDDIA QALALIGVQP VWDMASRRVT GYEIVPPAKL ARPRVDVTLR I SGFFRDAF PEQIALFDKA VRAVGALDED VEDNPIAARM KAEQARLVAG GADPQTAERR AGYRVFGSKP GAYGAGLQAL ID ENGWAGR NDLAEAWLVW GGYAYGAGEE GQAERGLLEE RLRSVQAVVQ NQDNREHDLL DSDDYYQFEG GMAATVESLT GAM PSVYHN DHSRPEKPVI RALEEELSRV VRGRAANPKW IAGVMRHGYK GAAEIAATVD YLFAFAATTG KVGNHHFEAV YQAY IADRA VHDFMAEKNP AALAETAAKL NEAIERGFWT PRSNSARFEL ENLSVHLQKL NPERAING

UniProtKB: Cobaltochelatase subunit CobN

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Macromolecule #2: COBALT (II) ION

MacromoleculeName: COBALT (II) ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: CO
Molecular weightTheoretical: 58.933 Da

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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: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207001
Initial angle assignmentType: OTHER
Final angle assignmentType: COMMON LINE

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