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- EMDB-73596: Structure of the long chain acyl-CoA carboxylase complex from Myc... -

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Basic information

Entry
Database: EMDB / ID: EMD-73596
TitleStructure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound
Map dataUnsharpened map
Sample
  • Complex: Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound
    • Protein or peptide: x 6 types
  • Ligand: x 6 types
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 / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
: / KipI family / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Biotin-dependent acetyl-/propionyl-coenzyme A carboxylase epsilon subunit / Acyl-CoA carboxylase epsilon subunit ...: / KipI family / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / 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 / Cyclophilin-like domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Allophanate hydrolase subunit 2 / Allophanate hydrolase subunit 1 / 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: 2.9 Å
AuthorsLiang Y / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT191893 Canada
CitationJournal: To Be Published
Title: Structural basis for substrate specificity and MSMEG_0435-0436 binding by the mycobacterial long-chain acyl-CoA carboxylase complex
Authors: Liang Y / Rubinstein JL
History
DepositionOct 26, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73596.png

Downloads & links

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Map

FileDownload / File: emd_73596.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.5578595 - 0.98254114
Average (Standard dev.)-0.00010140099 (±0.036793612)
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: Sharpened map

Fileemd_73596_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73596_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_73596_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 : Structure of the long chain acyl-CoA carboxylase complex from Myc...

EntireName: Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound
Components
  • Complex: Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
    • Protein or peptide: Acetyl-/propionyl-coenzyme A carboxylase AccE5
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
    • Protein or peptide: Allophanate hydrolase subunit 2
    • Protein or peptide: Allophanate hydrolase subunit 1
  • Ligand: S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (11E,14E,16E)-icosa-11,14,16-trienethioate (non-preferred name)
  • Ligand: propionyl Coenzyme A
  • Ligand: BIOTIN
  • Ligand: BICARBONATE ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Structure of the long chain acyl-CoA carboxylase complex from Myc...

SupramoleculeName: Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 980 KDa

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

MacromoleculeName: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: biotin carboxylase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 63.215176 KDa
SequenceString: MANHASSKIS KVLVANRGEI AVRVIRAAKD AGLASVAVYA EPDADAPHVR LADEAFALGG QTSAESYLVF EKILDAAEKS GANAIHPGY GFLSENADFA QAVIDAGLIW IGPSPQSIRD LGDKVTARHI AARAKAPLVP GTPDPVKDAD EVVAFAKEHG V PVAIKAAF ...String:
MANHASSKIS KVLVANRGEI AVRVIRAAKD AGLASVAVYA EPDADAPHVR LADEAFALGG QTSAESYLVF EKILDAAEKS GANAIHPGY GFLSENADFA QAVIDAGLIW IGPSPQSIRD LGDKVTARHI AARAKAPLVP GTPDPVKDAD EVVAFAKEHG V PVAIKAAF GGGGRGMKVA RTLEEIPELF ESATREAIAA FGRGECFVER YLDKPRHVEA QVIADQHGNV VVAGTRDCSL QR RFQKLVE EAPAPFLTDA QRKEIHESAK RICKEAGYYG AGTVEYLVGQ DGLISFLEVN TRLQVEHPVT EETSGIDLVR QQF KIANGE PLDITEDPTP RGHSFEFRIN GEDAGRGFLP APGPVTKFVA PTGPGVRMDS GVETGSVIGG QFDSMLAKLI VTGA TREEA LERSRRALAE FTVEGLATVI PFHRAVVSDP AFIGDGEKFD VHTRWIETEW NNTVEPFTGG DPIEEEDTVP RQTVV VEVG GRRLEVSLPG DLAIGGGGGA AAPGVVRKKP KPRKRGGGGA KAASGDAVTA PMQGTVVKVA VEEGQEVSAG DLVVVL EAM KMENPVTAHK DGTITGLAVE AGAAITQGTV IAEIK

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

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Macromolecule #2: Acetyl-/propionyl-coenzyme A carboxylase AccE5

MacromoleculeName: Acetyl-/propionyl-coenzyme A carboxylase AccE5 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 10.357693 KDa
SequenceString:
MSGANDSTTV SGEVQADVTD EAKADHEAHI KVLRGEPTPE EMAALMAVLA SAGGGPAEPV KKERNMWGHP VDKLRYSVFS WQRVTLLER THMRR

UniProtKB: Acetyl-/propionyl-coenzyme A carboxylase AccE5

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Macromolecule #3: Propionyl-CoA carboxylase beta chain

MacromoleculeName: Propionyl-CoA carboxylase beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 56.23407 KDa
SequenceString: MTNKTTAELL AELREKLELA KEPGGEKAVA KREKKGIPSA RARINALLDP GSFIEIGALA KTPGDPNALY GDGVVTGRGT IDGRPVGVF SHDQTVFQGS VGEMFGRKVA RLMEWVAMVG CPIIGINDSA GARIQDAVTS LAWYAELGRR HEMLRGLVPE I SLIFGKCA ...String:
MTNKTTAELL AELREKLELA KEPGGEKAVA KREKKGIPSA RARINALLDP GSFIEIGALA KTPGDPNALY GDGVVTGRGT IDGRPVGVF SHDQTVFQGS VGEMFGRKVA RLMEWVAMVG CPIIGINDSA GARIQDAVTS LAWYAELGRR HEMLRGLVPE I SLIFGKCA GGAVYSPIQT DLLVAVRDQG YMFITGPDVI KDVTGEDVTF DELGGADEQA KRGNIHKVVN SEAEAYQYVR DY LSFLPSN HFDNPPIVNP GMEPEITPHD LELDSIVPDA DNMAYDMHEI LLRIFDDGDV FEIAEQRGPA MITAFARVDG HPV GVIANQ PMVLSGAIDN EASDKAASFI RFCDSYNLPL VFVVDTPGAM PGVAEEKGGI IKRGGRFFNA IVEADVPKVT VIIR KAYGG GYAVMGSKQL SADLNFAWPT ARIAVIGAEG AAQLLVKRFP DPNAPEVQKI RDDFIEGYNL NMATPWIAAE RGYID AVIQ PHETRLLLRK SLRLLRDKQN GPKVQRKHGL LPL

UniProtKB: Propionyl-CoA carboxylase beta chain

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Macromolecule #4: Propionyl-CoA carboxylase beta chain

MacromoleculeName: Propionyl-CoA carboxylase beta chain / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: propionyl-CoA carboxylase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 58.488074 KDa
SequenceString: MTSVTEPSAE HQVDIHTTAG KLADLKRRTE ETLHPVGEAA VDKVHAKGKL TARERILALL DEGSFVELDA LAKHRSTNFG LEKNRPLGD GVITGYGTID GRDVCIFSQD ATVFGGSLGE VYGEKIVKVQ ELAIKTGRPL IGINDGAGAR IQEGVVSLGL Y SRIFHNNI ...String:
MTSVTEPSAE HQVDIHTTAG KLADLKRRTE ETLHPVGEAA VDKVHAKGKL TARERILALL DEGSFVELDA LAKHRSTNFG LEKNRPLGD GVITGYGTID GRDVCIFSQD ATVFGGSLGE VYGEKIVKVQ ELAIKTGRPL IGINDGAGAR IQEGVVSLGL Y SRIFHNNI KASGVIPQIS LIMGAAAGGH VYSPALTDFV VMVDQTSQMF ITGPDVIKTV TGEDVTMEEL GGAHTHMAKS GT AHYVASG EQDAFDYVRD LLSYLPPNNY ADPPLYPVAI PEGSIEETLT DEDLELDTLI PDSPNQPYDM HEVITRILDD DEF LEVQAG YAGNIVVGFG RVEGRPVGIV ANQPTQFAGC LDINASEKAA RFIRTCDCFN IPIVLLVDVP GFLPGTDQEY NGII RRGAK LLYAYGEATV AKVTVITRKS YGGAYCVMGS KDMGADVVVA WPTAQIAVMG ASGAVGFVYR QQLKEAAKNG EDVDA LRLE LQQTYEDTLV NPYIAAERGY VDAVIPPSHT RGYVANALRL LERKIVQMPP KKHGNIPL

UniProtKB: Propionyl-CoA carboxylase beta chain

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Macromolecule #5: Allophanate hydrolase subunit 2

MacromoleculeName: Allophanate hydrolase subunit 2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 31.280223 KDa
SequenceString: MGTTLEVLRT GPLALVEDLG RPGLAHMGVT RSGAADRRSH TLANRLVANP GESATIEVTF GGFSARVCGG DVAIAVTGAD TDPAVNGIP FGTNSIHHVH DGQVISLGAP HSGLRSYLAV RGGIDVTPVL GSRSYDVMSA IGPSPLRPGD VLPVGEHTDE F PELDQAPV ...String:
MGTTLEVLRT GPLALVEDLG RPGLAHMGVT RSGAADRRSH TLANRLVANP GESATIEVTF GGFSARVCGG DVAIAVTGAD TDPAVNGIP FGTNSIHHVH DGQVISLGAP HSGLRSYLAV RGGIDVTPVL GSRSYDVMSA IGPSPLRPGD VLPVGEHTDE F PELDQAPV AAIAEDVVEL QVVPGPRDDW FVDPDILVRT NWLVTNRSDR VGMRLVGMPL EYRNPDRQLP SEGATRGAIQ VP PNGFPVI LGPDHPVTGG YPVIGVVTEE DIDKLGQVRP GQTVRLHWAY PRRPFET

UniProtKB: Allophanate hydrolase subunit 2

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Macromolecule #6: Allophanate hydrolase subunit 1

MacromoleculeName: Allophanate hydrolase subunit 1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 22.659801 KDa
SequenceString: MTLGTVHNYG DQALLLEFDS TAEVLAWTET LREAELLGVV DIVPAARTVL VKLAGPRYQA PTRQRLGKLR VRPEAITHQP PGDRVDVTI DVVYDGADLH EVASLTGMTP AQVIAAHTGT PWRVGFCGFA PGFAYLVDGD ARLQVPRRAE PRTSVPAGAV A LAGEFSGV ...String:
MTLGTVHNYG DQALLLEFDS TAEVLAWTET LREAELLGVV DIVPAARTVL VKLAGPRYQA PTRQRLGKLR VRPEAITHQP PGDRVDVTI DVVYDGADLH EVASLTGMTP AQVIAAHTGT PWRVGFCGFA PGFAYLVDGD ARLQVPRRAE PRTSVPAGAV A LAGEFSGV YPRQSPGGWQ LIGHTDAVMF DVNRDKPALL TPGMWVQFRA VG

UniProtKB: Allophanate hydrolase subunit 1

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Macromolecule #7: S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydrox...

MacromoleculeName: S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~- ...Name: S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (11E,14E,16E)-icosa-11,14,16-trienethioate (non-preferred name)
type: ligand / ID: 7 / Number of copies: 2 / Formula: A1CZD
Molecular weightTheoretical: 1.056002 KDa

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Macromolecule #8: propionyl Coenzyme A

MacromoleculeName: propionyl Coenzyme A / type: ligand / ID: 8 / Number of copies: 4 / Formula: 1VU
Molecular weightTheoretical: 823.597 Da
Chemical component information

ChemComp-191:
PROPIONYL COENZYME A

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Macromolecule #9: BIOTIN

MacromoleculeName: BIOTIN / type: ligand / ID: 9 / Number of copies: 5 / Formula: BTN
Molecular weightTheoretical: 244.311 Da
Chemical component information

ChemComp-BTN:
BIOTIN

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Macromolecule #10: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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Macromolecule #11: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / 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 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: 50.0 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 was generated ab initio in cryoSPARC v5.0.0-privatebeta
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.0-privatebeta) / Number images used: 10016
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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