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- EMDB-10770: Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA -

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Basic information

Entry
Database: EMDB / ID: EMD-10770
TitlePropionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA
Map datapropionyl-CoA carboxylase of Methylorubrum extorquens AM1
Sample
  • Complex: Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
    • Protein or peptide: Propionyl-CoA carboxylase alpha subunit
  • Ligand: COENZYME A
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
Keywordsbiotin dependent / ATP dependent / propionyl-CoA / heterododecamer / CO2 fixation / LIGASE
Function / homology
Function and homology information


propionyl-CoA carboxylase / propionyl-CoA carboxylase activity / lipid catabolic process / ATP binding / metal ion binding
Similarity search - Function
Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain ...Propionyl-coenzyme A carboxylase, BT domain / Propionyl-coenzyme A carboxylase BT domain / : / : / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Propionyl-CoA carboxylase beta chain / propionyl-CoA carboxylase
Similarity search - Component
Biological speciesMethylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsSchuller JM / Schuller SK
Funding support Germany, 2 items
OrganizationGrant numberCountry
European CommissionFET-Open 686330 Germany
German Research Foundation (DFG)SCHU 3364/1-1 Germany
CitationJournal: Nat Catal / Year: 2021
Title: A new-to-nature carboxylation module to improve natural and synthetic CO2 fixation
Authors: Scheffen M / Marchal DG / Beneyton T / Schuller SK / Klose M / Diehl C / Lehmann J / Pfister P / Carrillo M / He H / Aslan S / Cortina NS / Claus P / Bollschweiler D / Baret JC / Schuller JM ...Authors: Scheffen M / Marchal DG / Beneyton T / Schuller SK / Klose M / Diehl C / Lehmann J / Pfister P / Carrillo M / He H / Aslan S / Cortina NS / Claus P / Bollschweiler D / Baret JC / Schuller JM / Zarzycki J / Bar-Even A / Erb TJ
History
DepositionMar 17, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.23
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.23
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ybp
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ybp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10770.png

Downloads & links

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Map

FileDownload / File: emd_10770.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpropionyl-CoA carboxylase of Methylorubrum extorquens AM1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 256 pix.
= 302.08 Å		1.18 Å/pix.
x 256 pix.
= 302.08 Å		1.18 Å/pix.
x 256 pix.
= 302.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23 / Movie #1: 0.23
Minimum - Maximum-0.60109526 - 1.2886994
Average (Standard dev.)0.008079505 (±0.0587024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 302.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.181.181.18
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z302.080302.080302.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.6011.2890.008

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Supplemental data

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Sample components

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Entire : Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA

EntireName: Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA
Components
  • Complex: Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
    • Protein or peptide: Propionyl-CoA carboxylase alpha subunit
  • Ligand: COENZYME A
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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Supramolecule #1: Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA

SupramoleculeName: Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Molecular weightTheoretical: 740 KDa

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Macromolecule #1: Propionyl-CoA carboxylase beta chain

MacromoleculeName: Propionyl-CoA carboxylase beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Molecular weightTheoretical: 56.060008 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKDILEKLEE RRAQARLGGG EKRLEAQHKR GKLTARERIE LLLDHGSFEE FDMFVQHRST DFGMEKQKIP GDGVVTGWGT VNGRTVFLF SKDFTVFGGS LSEAHAAKIV KVQDMALKMR APIIGIFDAG GARIQEGVAA LGGYGEVFRR NVAASGVIPQ I SVIMGPCA ...String:
MKDILEKLEE RRAQARLGGG EKRLEAQHKR GKLTARERIE LLLDHGSFEE FDMFVQHRST DFGMEKQKIP GDGVVTGWGT VNGRTVFLF SKDFTVFGGS LSEAHAAKIV KVQDMALKMR APIIGIFDAG GARIQEGVAA LGGYGEVFRR NVAASGVIPQ I SVIMGPCA GGDVYSPAMT DFIFMVRDTS YMFVTGPDVV KTVTNEVVTA EELGGAKVHT SKSSIADGSF ENDVEAILQI RR LLDFLPA NNIEGVPEIE SFDDVNRLDK SLDTLIPDNP NKPYDMGELI RRVVDEGDFF EIQAAYARNI ITGFGRVEGR TVG FVANQP LVLAGVLDSD ASRKAARFVR FCNAFSIPIV TFVDVPGFLP GTAQEYGGLI KHGAKLLFAY SQATVPLVTI ITRK AFGGA YDVMASKHVG ADLNYAWPTA QIAVMGAKGA VEIIFRAEIG DADKIAERTK EYEDRFLSPF VAAERGYIDE VIMPH STRK RIARALGMLR TKEMEQPWKK HDNIPL

UniProtKB: Propionyl-CoA carboxylase beta chain

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Macromolecule #2: Propionyl-CoA carboxylase alpha subunit

MacromoleculeName: Propionyl-CoA carboxylase alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Molecular weightTheoretical: 71.986961 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFDKILIANR GEIACRIIKT AQKMGIKTVA VYSDADRDAV HVAMADEAVH IGPAPAAQSY LLIEKIIDAC KQTGAQAVHP GYGFLSERE SFPKALAEAG IVFIGPNPGA IAAMGDKIES KKAAAAAEVS TVPGFLGVIE SPEHAVTIAD EIGYPVMIKA S AGGGGKGM ...String:
MFDKILIANR GEIACRIIKT AQKMGIKTVA VYSDADRDAV HVAMADEAVH IGPAPAAQSY LLIEKIIDAC KQTGAQAVHP GYGFLSERE SFPKALAEAG IVFIGPNPGA IAAMGDKIES KKAAAAAEVS TVPGFLGVIE SPEHAVTIAD EIGYPVMIKA S AGGGGKGM RIAESADEVA EGFARAKSEA SSSFGDDRVF VEKFITDPRH IEIQVIGDKH GNVIYLGERE CSIQRRNQKV IE EAPSPLL DEETRRKMGE QAVALAKAVN YDSAGTVEFV AGQDKSFYFL EMNTRLQVEH PVTEMITGLD LVELMIRVAA GEK LPLSQD QVKLDGWAVE SRVYAEDPTR NFLPSIGRLT TYQPPEEGPL GGAIVRNDTG VEEGGEIAIH YDPMIAKLVT WAPT RLEAI EAQATALDAF AIEGIRHNIP FLATLMAHPR WRDGRLSTGF IKEEFPEGFI APEPEGPVAH RLAAVAAAID HKLNI RKRG ISGQMRDPSL LTFQRERVVV LSGQRFNVTV DPDGDDLLVT FDDGTTAPVR SAWRPGAPVW SGTVGDQSVA IQVRPL LNG VFLQHAGAAA EARVFTRREA ELADLMPVKE NAGSGKQLLC PMPGLVKQIM VSEGQEVKNG EPLAIVEAMK MENVLRA ER DGTISKIAAK EGDSLAVDAV ILEFA

UniProtKB: propionyl-CoA carboxylase

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Macromolecule #3: COENZYME A

MacromoleculeName: COENZYME A / type: ligand / ID: 3 / Number of copies: 6 / Formula: COA
Molecular weightTheoretical: 767.534 Da
Chemical component information

ChemComp-COA:
COENZYME A

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Macromolecule #4: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

MacromoleculeName: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
type: ligand / ID: 4 / Number of copies: 6 / Formula: BTI
Molecular weightTheoretical: 228.311 Da
Chemical component information

ChemComp-BTI:
5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL

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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: 7.8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 50.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77714
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

Initial modelPDB ID:

3n6r


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6ybp:
Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA

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