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- EMDB-64238: CryoEM structure of Brucella melitensis CobS-CobT complex with AM... -

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Basic information

Entry
Database: EMDB / ID: EMD-64238
TitleCryoEM structure of Brucella melitensis CobS-CobT complex with AMPPNP (conformation 5)
Map data
Sample
  • Complex: CobST-AMPPNP complex 5
    • Protein or peptide: Cobaltochelatase subunit CobS
    • Protein or peptide: Cobaltochelatase subunit CobT
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsCobalt chelatase / CobS-CobT complex / AMPPNP / LIGASE
Function / homology
Function and homology information


cobaltochelatase / cobaltochelatase activity / cobalamin biosynthetic process / ATP hydrolysis activity / ATP binding
Similarity search - Function
Cobalt chelatase, CobT subunit / Cobalamin biosynthesis protein CobT VWA domain / Cobalamin biosynthesis protein CobT / Cobalamin biosynthesis protein CobT VWA domain / Cobaltochelatase subunit CobS / Cobaltochelatase subunit CobS N-terminal domain / Cobaltochelatase CobS subunit N terminal / : / : / ATPase, dynein-related, AAA domain ...Cobalt chelatase, CobT subunit / Cobalamin biosynthesis protein CobT VWA domain / Cobalamin biosynthesis protein CobT / Cobalamin biosynthesis protein CobT VWA domain / Cobaltochelatase subunit CobS / Cobaltochelatase subunit CobS N-terminal domain / Cobaltochelatase CobS subunit N terminal / : / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cobaltochelatase subunit CobT / Cobaltochelatase subunit CobS
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 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_64238.png

Downloads & links

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Map

FileDownload / File: emd_64238.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: 0.02
Minimum - Maximum-0.0017088489 - 2.4108396
Average (Standard dev.)0.0018451662 (±0.032534923)
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_64238_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_64238_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 : CobST-AMPPNP complex 5

EntireName: CobST-AMPPNP complex 5
Components
  • Complex: CobST-AMPPNP complex 5
    • Protein or peptide: Cobaltochelatase subunit CobS
    • Protein or peptide: Cobaltochelatase subunit CobT
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: CobST-AMPPNP complex 5

SupramoleculeName: CobST-AMPPNP complex 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 6 / 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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Macromolecule #2: Cobaltochelatase subunit CobT

MacromoleculeName: Cobaltochelatase subunit CobT / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Brucella melitensis (bacteria)
Molecular weightTheoretical: 70.722406 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSGQMSGIGD NSRDRKTGPV DSEPFKRAIT ACVRAISGDH EMEVAFSHDR PALSANRARL PDLPKRPTAH DIAVTRGLGD SMALRQARH NPRIHAALAP EGKQARAIFD AVEQARVEAI GARAMAGVAD NLSTMLADKY SRANFSAVTT KEDAPLEEAV S LLLREKLT ...String:
MSGQMSGIGD NSRDRKTGPV DSEPFKRAIT ACVRAISGDH EMEVAFSHDR PALSANRARL PDLPKRPTAH DIAVTRGLGD SMALRQARH NPRIHAALAP EGKQARAIFD AVEQARVEAI GARAMAGVAD NLSTMLADKY SRANFSAVTT KEDAPLEEAV S LLLREKLT GRPAPAEAGQ VLELWRDWIE QKASADIARL GENLEDQQAF ARTVRDMLAS MDMAEELSQE EPSDDEEQND EQ TPDSDEN EEGGDENQEG SDSAESEESD SSSDEGEQGE MDAADASADE MDDSEDIDAE TPGDTRRPNQ PFANFAEHVD YKV FTREFD EEVEATDLCD EAELDRLRGF LDKQLANLQG VVGRLANRLQ RRLMAQQNRS WDFDLEEGYL DSARLVRIVI DPTQ PLSYK QERDTDFRDT VVTLVLDNSG SMRGRPITVA ATCADILART LERCGVKVEI LGFTTKAWKG GQSREAWLGR GKPAN PGRL NDLRHIVYKS ADAPWRRARR NLGLMMREGL LKENIDGEAL IWAHQRLLGR PEQRKILMMI SDGAPVDDST LSVNPG NYL ERHLRAVIEE IETRSPVELI AIGIGHDVTR YYQRAVTIVD AEELAGAMTE QLASLFEEQG AAASVRGRRR AGRR

UniProtKB: Cobaltochelatase subunit CobT

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 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

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65726
Initial angle assignmentType: OTHER
Final angle assignmentType: COMMON LINE

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