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- PDB-9zvm: Dimer structure of Thlaspi arvense plastid biotin carboxylase -

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Basic information

Entry
Database: PDB / ID: 9zvm
TitleDimer structure of Thlaspi arvense plastid biotin carboxylase
ComponentsMaltodextrin-binding protein,Biotin carboxylase
KeywordsLIGASE / homodimer / carboxylase
Function / homology
Function and homology information


biotin carboxylase / biotin carboxylase activity / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chloroplast / fatty acid biosynthetic process / outer membrane-bounded periplasmic space ...biotin carboxylase / biotin carboxylase activity / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / chloroplast / fatty acid biosynthetic process / outer membrane-bounded periplasmic space / ATP binding / metal ion binding
Similarity search - Function
Acetyl-CoA carboxylase, biotin carboxylase / : / 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. ...Acetyl-CoA carboxylase, biotin carboxylase / : / 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 / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Biotin carboxylase / Maltodextrin-binding protein
Similarity search - Component
Biological speciesThlaspi arvense (field pennycress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsMadison, H.J. / Van Doren, S.R. / Yokom, A.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Biochem J / Year: 2026
Title: Oligomeric assemblies of plant biotin carboxylase revealed by cryo-EM and cross-linking.
Authors: Hunter J Madison / Luke Dunn / Youngki You / Gabriel Lemes Jorge / Ljiljana Paša-Tolić / Jay J Thelen / Steven R Van Doren / Adam L Yokom /
Abstract: Due to the interest in fatty acid synthesis by oilseed crops, we conducted structural studies of the biotin carboxylase (BC) subunit of the plastid acetyl-CoA carboxylase. Acetyl-CoA carboxylase ...Due to the interest in fatty acid synthesis by oilseed crops, we conducted structural studies of the biotin carboxylase (BC) subunit of the plastid acetyl-CoA carboxylase. Acetyl-CoA carboxylase catalyzes the first committed step in the fatty acid synthesis pathway and is highly regulated. Cryo-electron microscopy revealed that Thlaspi arvense (pennycress) BC forms a symmetric dimer and contains a subpopulation of a dimer-of-dimers. The domain of BC that closes over the catalytic cleft (the B-domain) appears to be dynamic, judging from the b-factors, normal mode analysis of BC structures, and its high susceptibility to acetylation. An increase in the BC concentration decreased the reactivity of the B-domain, however, suggesting structural hindrance. The partial protection of the B-domain was consistent with cross-links that formed between dimers of BC using a cross-linker cleavable in the mass spectrometer. Cross-links guided HADDOCK docking calculations suggesting a dimer of dimers of BC that is asymmetric, staggered, and tilted between dimers, with conservation in the interface. In contrast, a minimal population of a symmetric dimer of dimers with a small, non-conserved interface was observed by cryo-EM. Taken together, our structural models are the first for Brassicaceae family BC homologs and are the first from plants. These models suggest dimer interactions that might contribute to larger oligomers of BC and influence associations with other subunits of the heteromeric acetyl-CoA carboxylase.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionDec 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Maltodextrin-binding protein,Biotin carboxylase
D: Maltodextrin-binding protein,Biotin carboxylase


Theoretical massNumber of molelcules
Total (without water)189,3272
Polymers189,3272
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Maltodextrin-binding protein,Biotin carboxylase / Acetyl-coenzyme A carboxylase biotin carboxylase subunit A


Mass: 94663.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thlaspi arvense (field pennycress)
Gene: malE, malE_1, ABE91_029440, ACU57_23670, B6R31_000964, BANRA_00036, BANRA_02908, BANRA_05111, BCB93_001091, BG944_002391, BGM66_004246, BK300_12795, BMT50_07545, BMT91_12860, BRV02_002252, ...Gene: malE, malE_1, ABE91_029440, ACU57_23670, B6R31_000964, BANRA_00036, BANRA_02908, BANRA_05111, BCB93_001091, BG944_002391, BGM66_004246, BK300_12795, BMT50_07545, BMT91_12860, BRV02_002252, BTB68_002078, BTQ06_17300, BvCmsKKP061_03224, C0P57_003867, C1Q91_002164, C2R31_001890, C3F40_15210, C6669_07330, C719_004008, C7B02_13920, C9160_08140, C9194_00175, CCS08_02575, CF22_001770, CG702_16655, CIG67_12040, CQ842_10105, CQ842_11395, CR538_23895, CTR35_003815, CV83915_02005, CWS33_15915, D4M65_12865, DIV22_28370, DL968_20910, DNX30_07695, DS732_01860, DTL43_19585, E2863_04856, E4K51_08355, E5H86_20640, E6D34_15030, EAI46_20350, ECs5017, EIZ93_13775, EN85_000970, EPS97_17355, ExPECSC038_04540, EXX87_20045, F9461_21760, FGAF848_44030, FIJ20_18085, FJQ40_13885, FOI11_015465, FOI11_20215, FPS11_04610, FV293_00135, FWK02_22115, G3V95_18070, G4A38_02205, G4A47_04495, GAI89_05080, GAJ12_13200, GKF66_19285, GNW61_17855, GOP25_18965, GP965_07770, GP975_07695, GP979_10140, GQA06_09595, GQM04_22095, GQM21_08325, GQN24_10395, GRW05_14255, GRW24_12940, GUC01_08260, HEP30_015080, HHH44_003952, HKA49_001043, HLX92_13085, HMV95_14740, HV109_22180, HV209_20940, HVW43_14700, HVY77_23840, HX136_23390, I6H02_15990, IDONEFKE_03431, J0541_001933, J5U05_001620, J8F57_003138, JNA65_10350, JNA68_19710, JNP96_01525, NCTC10279_03406, NCTC10418_07064, NCTC10429_00012, NCTC10865_05806, NCTC11126_02082, NCTC11181_01902, NCTC13148_04480, NCTC8009_08341, NCTC8179_05034, NCTC8333_05503, NCTC8500_05253, NCTC8622_01707, NCTC8960_02276, NCTC8985_03950, NCTC9706_01951, NCTC9962_03706, NOI85_19130, NQD80_13745, NY836_27910, OFN31_11500, P6223_003521, Q2V20_09975, QDW62_24215, RZR61_19445, SAMEA3472044_04499, SAMEA3752557_02201, TUM18780_41180, WR15_07725, TAV2_LOCUS20518
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3SHQ8, UniProt: A0AAU9SW86, biotin carboxylase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: homodimeric complex of biotin carboxylase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.052 MDa / Experimental value: NO
Source (natural)Organism: Thlaspi arvense (field pennycress)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 DE3
Buffer solutionpH: 8
Details: 50mM HEPES pH 8.0, 4mM MgCl2, 5% glycerol, 0.5mM TCEP
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
24 mMmagnesium chlorideMgCl21
35 %glycerolC3H8O31
40.5 mMTCEPC9H15O6P1
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7Coot0.9.8.6model fitting
8ISOLDE1.1model fitting
12cryoSPARCclassification
13cryoSPARC3D reconstruction
14PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 703126
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142000 / Num. of class averages: 50 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 45.99 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00277102
ELECTRON MICROSCOPYf_angle_d0.5279612
ELECTRON MICROSCOPYf_chiral_restr0.04431066
ELECTRON MICROSCOPYf_plane_restr0.00451272
ELECTRON MICROSCOPYf_dihedral_angle_d4.6989982

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