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- EMDB-74880: Dimer structure of Thlaspi arvense plastid biotin carboxylase -

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Basic information

Entry
Database: EMDB / ID: EMD-74880
TitleDimer structure of Thlaspi arvense plastid biotin carboxylase
Map data
Sample
  • Complex: homodimeric complex of biotin carboxylase
    • Protein or peptide: Maltodextrin-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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsMadison HJ / Van Doren SR / Yokom AL
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: 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, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74880.png

Downloads & links

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Map

FileDownload / File: emd_74880.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 256 pix.
= 248.32 Å		0.97 Å/pix.
x 256 pix.
= 248.32 Å		0.97 Å/pix.
x 256 pix.
= 248.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.6877143 - 2.9727526
Average (Standard dev.)0.00057525607 (±0.048307016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 248.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_74880_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74880_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : homodimeric complex of biotin carboxylase

EntireName: homodimeric complex of biotin carboxylase
Components
  • Complex: homodimeric complex of biotin carboxylase
    • Protein or peptide: Maltodextrin-binding protein,Biotin carboxylase

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Supramolecule #1: homodimeric complex of biotin carboxylase

SupramoleculeName: homodimeric complex of biotin carboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thlaspi arvense (field pennycress)
Molecular weightTheoretical: 52 KDa

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Macromolecule #1: Maltodextrin-binding protein,Biotin carboxylase

MacromoleculeName: Maltodextrin-binding protein,Biotin carboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: biotin carboxylase
Source (natural)Organism: Thlaspi arvense (field pennycress)
Molecular weightTheoretical: 94.663461 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY ...String:
MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NKGETAMTIN GPWAWSNIDT SK VNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPLGAVALKS YEEELAKDPR IAA TMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TNSSSNNNNN NNNNNLGIEG RGENLYFQGS GDKI LVANR GEIAVRVIRT AHEMGIPCVA VYSTIDKDAL HVKLADEAVC IGEAPSNQSY LLIPNVLSAA ISRGCTMLHP GYGFL AENA LFVEMCRDHR INFIGPNPDS IRVMGDKSTA RETMKNAGVP TVPGSDGLLQ STEEGVRLAN EIGFPVMIKA TAGGGG RGM RLANEPSEFV KLLQQAKSEA AAAFGNDGVY LEKYVQNPRH IEFQILADKF GNVVHFGERD CSIQRRNQKL LEEAPSP AL TPELRKAMGD AAVAAAASIG YIGVGTVEFL LDERGSFYFM EMNTRIQVEH PVTEMIYSVD LIEEQIRVAM GEKLRYKQ E EIVLRGHSIE CRINAEDPFK GFRPGPGRIT SYLPSGGPFV RMDSHVYPDY VVPPSYDSLL GKLIVWAPTR ERAIERMKR ALNDTIITGV PTTIEYHKLI LEVEDFKNGK VDTAFIPKHE EELAEPQEIV SVKDLTNVAA

UniProtKB: Maltodextrin-binding protein, Biotin carboxylase

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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

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
4.0 mMMgCl2magnesium chloride
5.0 %C3H8O3glycerol
0.5 mMC9H15O6PTCEP

Details: 50mM HEPES pH 8.0, 4mM MgCl2, 5% glycerol, 0.5mM TCEP
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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 / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.3 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 703126
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold 3 generated model
Final reconstructionNumber classes used: 50 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 142000
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 50 / Avg.num./class: 2844 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot (ver. 0.9.8.6)
Output model

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

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