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- EMDB-74881: Tetramer structure of Thlaspi arvense plastid biotin carboxylase -

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Basic information

Entry
Database: EMDB / ID: EMD-74881
TitleTetramer structure of Thlaspi arvense plastid biotin carboxylase
Map data
Sample
  • Complex: homotetrameric complex of biotin carboxylase
    • Protein or peptide: biotin carboxylase
Keywordsligase / homotetramer / carboxylase
Biological speciesThlaspi arvense (field pennycress)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.1 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_74881.png

Downloads & links

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Map

FileDownload / File: emd_74881.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 180 pix.
= 174.6 Å		0.97 Å/pix.
x 180 pix.
= 174.6 Å		0.97 Å/pix.
x 180 pix.
= 174.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.4316171 - 0.7335239
Average (Standard dev.)0.0013995172 (±0.021564152)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 174.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_74881_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74881_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : homotetrameric complex of biotin carboxylase

EntireName: homotetrameric complex of biotin carboxylase
Components
  • Complex: homotetrameric complex of biotin carboxylase
    • Protein or peptide: biotin carboxylase

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Supramolecule #1: homotetrameric complex of biotin carboxylase

SupramoleculeName: homotetrameric 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: biotin carboxylase

MacromoleculeName: biotin carboxylase / type: protein_or_peptide / ID: 1 / Details: MBP-tagged biotin carboxylase / Enantiomer: LEVO / EC number: biotin carboxylase
Source (natural)Organism: Thlaspi arvense (field pennycress)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDKL YPFTWDAVRY NGKLIAYPIA VEALSLIYNK DLLPNPPKTW EEIPALDKEL KAKGKSALMF NLQEPYFTWP LIAADGGYAF ...String:
MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDKL YPFTWDAVRY NGKLIAYPIA VEALSLIYNK DLLPNPPKTW EEIPALDKEL KAKGKSALMF NLQEPYFTWP LIAADGGYAF KYENGKYDIK DVGVDNAGAK AGLTFLVDLI KNKHMNADTD YSIAEAAFNK GETAMTINGP WAWSNIDTSK VNYGVTVLPT FKGQPSKPFV GVLSAGINAA SPNKELAKEF LENYLLTDEG LEAVNKDKPL GAVALKSYEE ELAKDPRIAA TMENAQKGEI MPNIPQMSAF WYAVRTAVIN AASGRQTVDE ALKDAQTNSS SNNNNNNNNN NLGIEGRGEN LYFQGSGDKI LVANRGEIAV RVIRTAHEMG IPCVAVYSTI DKDALHVKLA DEAVCIGEAP SNQSYLLIPN VLSAAISRGC TMLHPGYGFL AENALFVEMC RDHRINFIGP NPDSIRVMGD KSTARETMKN AGVPTVPGSD GLLQSTEEGV RLANEIGFPV MIKATAGGGG RGMRLANEPS EFVKLLQQAK SEAAAAFGND GVYLEKYVQN PRHIEFQILA DKFGNVVHFG ERDCSIQRRN QKLLEEAPSP ALTPELRKAM GDAAVAAAAS IGYIGVGTVE FLLDERGSFY FMEMNTRIQV EHPVTEMIYS VDLIEEQIRV AMGEKLRYKQ EEIVLRGHSI ECRINAEDPF KGFRPGPGRI TSYLPSGGPF VRMDSHVYPD YVVPPSYDSL LGKLIVWAPT RERAIERMKR ALNDTIITGV PTTIEYHKLI LEVEDFKNGK VDTAFIPKHE EELAEPQEIV SVKDLTNVAA

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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
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: 10880
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2080
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
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)

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