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- EMDB-73583: Locally refined map of the lower two AccA3 clusters of the long c... -

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Entry
Database: EMDB / ID: EMD-73583
TitleLocally refined map of the lower two AccA3 clusters of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, and propionyl-CoA
Map data
Sample
  • Complex: Locally refined map of the lower two AccA3 clusters of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, and propionyl-CoA
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit AccA3
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase epsilon subunit AccE
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase beta4 subunit AccD4
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase beta5 subunit AccD5
KeywordsCarboxylase / transferase / lipid synthesis / mycolic acid synthesis / LIGASE
Function / homology
Function and homology information


propionyl-CoA carboxylase / biotin carboxylase / propionyl-CoA carboxylase activity / acetyl-CoA carboxylase complex / biotin carboxylase activity / acetyl-CoA carboxylase activity / carbon fixation / fatty acid biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain ...Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit / : / : / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-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 / ATP-grasp fold, subdomain 1 / 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
Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit / Acetyl-/propionyl-coenzyme A carboxylase AccE5 / Propionyl-CoA carboxylase beta chain / Propionyl-CoA carboxylase beta chain
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLiang Y / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT191893 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis for substrate specificity and MSMEG_0435-0436 binding by the mycobacterial long-chain acyl-CoA carboxylase complex.
Authors: Yingke Liang / Stephanie A Bueler / John L Rubinstein /
Abstract: The presence of mycolic acid is a defining feature of the mycobacterial cell wall, which provides a highly impermeable barrier to many antibiotics. Biosynthesis of this fatty acid, as well as ...The presence of mycolic acid is a defining feature of the mycobacterial cell wall, which provides a highly impermeable barrier to many antibiotics. Biosynthesis of this fatty acid, as well as tuberculostearic acid, requires precursor molecules produced by the essential long-chain acyl-coenzyme A (CoA) carboxylase (LCC) complex. The LCC complex catalyzes carboxylation of the α-carbon of long-chain acyl-CoA, but also short-chain acetyl-CoA and propionyl-CoA. The complex includes the subunits AccA3, which contains a biotin carboxylase (BC) domain and a biotin carboxyl carrier protein (BCCP) domain, the long-chain acyl-CoA carboxyltransferase AccD4, the short-chain acyl-CoA carboxyltransferase AccD5, and the incompletely characterized protein AccE. We used electron cryomicroscopy (cryo-EM) to determine structures of the LCC complex from . In the structures, two AccE subunits tether eight AccA3 subunits to an AccD4AccD5 heterohexamer core. Cryo-EM of the enzyme during catalysis reveals how AccD4 and AccD5 achieve substrate specificity, with AccD5 binding tightly to CoA and AccD4 binding long acyl chains. The BCCP domains of AccA3 undergo long-distance translocation to transfer a carboxyl group from the BC domain of AccA3 to the acyl-CoA substrate bound in AccD5. Further, we find that two copies of a protein complex formed from MSMEG_0435 and MSMEG_0436 can bind the LCC complex, sequestering the biotin moiety of BCCP domains near AccD5 and decreasing propionyl-CoA carboxylase activity. Rv0263c, the ortholog of MSMEG_0435, has a role in bacterial survival during transmission, suggesting that these proteins may regulate production of branched fatty acid precursors for the mycobacterial cell wall.
History
DepositionOct 26, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73583.png

Downloads & links

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Map

FileDownload / File: emd_73583.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 480 pix.
= 446.4 Å		0.93 Å/pix.
x 480 pix.
= 446.4 Å		0.93 Å/pix.
x 480 pix.
= 446.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.42962238 - 0.89186823
Average (Standard dev.)-0.00038256616 (±0.022240687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 446.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_73583_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73583_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73583_half_map_2.map
Projections & Slices
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Sample components

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Entire : Locally refined map of the lower two AccA3 clusters of the long c...

EntireName: Locally refined map of the lower two AccA3 clusters of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, and propionyl-CoA
Components
  • Complex: Locally refined map of the lower two AccA3 clusters of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, and propionyl-CoA
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit AccA3
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase epsilon subunit AccE
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase beta4 subunit AccD4
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase beta5 subunit AccD5

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Supramolecule #1: Locally refined map of the lower two AccA3 clusters of the long c...

SupramoleculeName: Locally refined map of the lower two AccA3 clusters of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, and propionyl-CoA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 870 KDa

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Macromolecule #1: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit AccA3

MacromoleculeName: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit AccA3
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: biotin carboxylase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MANHASSKIS KVLVANRGEI AVRVIRAAKD AGLASVAVYA EPDADAPHVR LADEAFALGG QTSAESYLV FEKILDAAEK SGANAIHPGY GFLSENADFA QAVIDAGLIW IGPSPQSIRD L GDKVTARH IAARAKAPLV PGTPDPVKDA DEVVAFAKEH GVPVAIKAAF ...String:
MANHASSKIS KVLVANRGEI AVRVIRAAKD AGLASVAVYA EPDADAPHVR LADEAFALGG QTSAESYLV FEKILDAAEK SGANAIHPGY GFLSENADFA QAVIDAGLIW IGPSPQSIRD L GDKVTARH IAARAKAPLV PGTPDPVKDA DEVVAFAKEH GVPVAIKAAF GGGGRGMKVA RT LEEIPEL FESATREAIA AFGRGECFVE RYLDKPRHVE AQVIADQHGN VVVAGTRDCS LQR RFQKLV EEAPAPFLTD AQRKEIHESA KRICKEAGYY GAGTVEYLVG QDGLISFLEV NTRL QVEHP VTEETSGIDL VRQQFKIANG EPLDITEDPT PRGHSFEFRI NGEDAGRGFL PAPGP VTKF VAPTGPGVRM DSGVETGSVI GGQFDSMLAK LIVTGATREE ALERSRRALA EFTVEG LAT VIPFHRAVVS DPAFIGDGEK FDVHTRWIET EWNNTVEPFT GGDPIEEEDT VPRQTVV VE VGGRRLEVSL PGDLAIGGGG GAAAPGVVRK KPKPRKRGGG GAKAASGDAV TAPMQGTV V KVAVEEGQEV SAGDLVVVLE AMKMENPVTA HKDGTITGLA VEAGAAITQG TVIAEIK

UniProtKB: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit

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Macromolecule #2: Biotin-dependent acyl-coenzyme A carboxylase epsilon subunit AccE

MacromoleculeName: Biotin-dependent acyl-coenzyme A carboxylase epsilon subunit AccE
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString:
MSGANDSTTV SGEVQADVTD EAKADHEAHI KVLRGEPTPE EMAALMAVLA SAGGGPAEPV KKERNMWGH PVDKLRYSVF SWQRVTLLER THMRR

UniProtKB: Acetyl-/propionyl-coenzyme A carboxylase AccE5

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Macromolecule #3: Biotin-dependent acyl-coenzyme A carboxylase beta4 subunit AccD4

MacromoleculeName: Biotin-dependent acyl-coenzyme A carboxylase beta4 subunit AccD4
type: protein_or_peptide / ID: 3 / Enantiomer: LEVO / EC number: ec: 6.4.1.-
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MTNKTTAELL AELREKLELA KEPGGEKAVA KREKKGIPSA RARINALLDP GSFIEIGALA KTPGDPNAL YGDGVVTGRG TIDGRPVGVF SHDQTVFQGS VGEMFGRKVA RLMEWVAMVG C PIIGINDS AGARIQDAVT SLAWYAELGR RHEMLRGLVP EISLIFGKCA ...String:
MTNKTTAELL AELREKLELA KEPGGEKAVA KREKKGIPSA RARINALLDP GSFIEIGALA KTPGDPNAL YGDGVVTGRG TIDGRPVGVF SHDQTVFQGS VGEMFGRKVA RLMEWVAMVG C PIIGINDS AGARIQDAVT SLAWYAELGR RHEMLRGLVP EISLIFGKCA GGAVYSPIQT DL LVAVRDQ GYMFITGPDV IKDVTGEDVT FDELGGADEQ AKRGNIHKVV NSEAEAYQYV RDY LSFLPS NHFDNPPIVN PGMEPEITPH DLELDSIVPD ADNMAYDMHE ILLRIFDDGD VFEI AEQRG PAMITAFARV DGHPVGVIAN QPMVLSGAID NEASDKAASF IRFCDSYNLP LVFVV DTPG AMPGVAEEKG GIIKRGGRFF NAIVEADVPK VTVIIRKAYG GGYAVMGSKQ LSADLN FAW PTARIAVIGA EGAAQLLVKR FPDPNAPEVQ KIRDDFIEGY NLNMATPWIA AERGYID AV IQPHETRLLL RKSLRLLRDK QNGPKVQRKH GLLPL

UniProtKB: Propionyl-CoA carboxylase beta chain

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Macromolecule #4: Biotin-dependent acyl-coenzyme A carboxylase beta5 subunit AccD5

MacromoleculeName: Biotin-dependent acyl-coenzyme A carboxylase beta5 subunit AccD5
type: protein_or_peptide / ID: 4 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MTSVTEPSAE HQVDIHTTAG KLADLKRRTE ETLHPVGEAA VDKVHAKGKL TARERILALL DEGSFVELD ALAKHRSTNF GLEKNRPLGD GVITGYGTID GRDVCIFSQD ATVFGGSLGE V YGEKIVKV QELAIKTGRP LIGINDGAGA RIQEGVVSLG LYSRIFHNNI ...String:
MTSVTEPSAE HQVDIHTTAG KLADLKRRTE ETLHPVGEAA VDKVHAKGKL TARERILALL DEGSFVELD ALAKHRSTNF GLEKNRPLGD GVITGYGTID GRDVCIFSQD ATVFGGSLGE V YGEKIVKV QELAIKTGRP LIGINDGAGA RIQEGVVSLG LYSRIFHNNI KASGVIPQIS LI MGAAAGG HVYSPALTDF VVMVDQTSQM FITGPDVIKT VTGEDVTMEE LGGAHTHMAK SGT AHYVAS GEQDAFDYVR DLLSYLPPNN YADPPLYPVA IPEGSIEETL TDEDLELDTL IPDS PNQPY DMHEVITRIL DDDEFLEVQA GYAGNIVVGF GRVEGRPVGI VANQPTQFAG CLDIN ASEK AARFIRTCDC FNIPIVLLVD VPGFLPGTDQ EYNGIIRRGA KLLYAYGEAT VAKVTV ITR KSYGGAYCVM GSKDMGADVV VAWPTAQIAV MGASGAVGFV YRQQLKEAAK NGEDVDA LR LELQQTYEDT LVNPYIAAER GYVDAVIPPS HTRGYVANAL RLLERKIVQM PPKKHGNI P L

UniProtKB: Propionyl-CoA carboxylase beta chain

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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

Concentration5 mg/mL
BufferpH: 6
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 35 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 8000 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.0-privatebeta) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Initial model generated ab initio in cryoSPARC v5.0.0-privatebeta
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.0-privatebeta) / Number images used: 46806
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0-privatebeta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0-privatebeta)
FSC plot (resolution estimation)

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