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- EMDB-55802: Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Prop... -

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Basic information

Entry
Database: EMDB / ID: EMD-55802
TitleCryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
Map data
Sample
  • Complex: Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
    • Protein or peptide: Acetyl-/propionyl-coenzyme A carboxylase AccE5
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
  • Ligand: propionyl Coenzyme A
KeywordsBio-dependent acyl-CoA carboxylase / long chain/short chain acyl-CoA carboxylase / TRANSFERASE
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: 2.4 Å
AuthorsMullapudi E / Thai HM / de Carvalho LPS / Wilmanns M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
Authors: Mullapudi E / Thai HM / de Carvalho LPS / Wilmanns M
History
DepositionNov 24, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55802.png

Downloads & links

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Map

FileDownload / File: emd_55802.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 560 pix.
= 380.8 Å		0.68 Å/pix.
x 560 pix.
= 380.8 Å		0.68 Å/pix.
x 560 pix.
= 380.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.058183372 - 0.17569472
Average (Standard dev.)0.0002407284 (±0.0060477112)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 380.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55802_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_55802_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 : Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Prop...

EntireName: Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
Components
  • Complex: Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
    • Protein or peptide: Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
    • Protein or peptide: Propionyl-CoA carboxylase beta chain
    • Protein or peptide: Acetyl-/propionyl-coenzyme A carboxylase AccE5
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL
  • Ligand: propionyl Coenzyme A

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Supramolecule #1: Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Prop...

SupramoleculeName: Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 800 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: 8 / 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: Propionyl-CoA carboxylase beta chain

MacromoleculeName: Propionyl-CoA carboxylase beta chain / type: protein_or_peptide / ID: 2 / 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 #3: Propionyl-CoA carboxylase beta chain

MacromoleculeName: Propionyl-CoA carboxylase beta chain / type: protein_or_peptide / ID: 3 / 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 #4: Acetyl-/propionyl-coenzyme A carboxylase AccE5

MacromoleculeName: Acetyl-/propionyl-coenzyme A carboxylase AccE5 / type: protein_or_peptide / ID: 4 / 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 #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / 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 #6: 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: 6 / Number of copies: 5 / 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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Macromolecule #7: propionyl Coenzyme A

MacromoleculeName: propionyl Coenzyme A / type: ligand / ID: 7 / Number of copies: 4 / Formula: 1VU
Molecular weightTheoretical: 823.597 Da
Chemical component information

ChemComp-191:
PROPIONYL COENZYME A

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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

Concentration4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris
150.0 mMNaClSodium chloride
2.0 mMDTTDTT
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6398521
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 52469
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9tdm:
Cryo-EM structure of AccA3/AccD4/AccD5/AccE5 in complex with Propionyl-CoA

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