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- EMDB-31053: Cryo-EM structure of Isocitrate lyase-1 from Candida albicans -

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Basic information

Entry
Database: EMDB / ID: EMD-31053
TitleCryo-EM structure of Isocitrate lyase-1 from Candida albicans
Map data
Sample
  • Complex: Isocitrate lyase
    • Protein or peptide: Isocitrate lyase
KeywordsIsocitrate lyase / glyoxylate cycle / ubiquitination / LYASE
Function / homology
Function and homology information


methylisocitrate lyase activity / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / peroxisome / metal ion binding
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.63 Å
AuthorsHiragi K / Nishio K
CitationJournal: J Struct Biol / Year: 2021
Title: Structural insights into the targeting specificity of ubiquitin ligase for S. cerevisiae isocitrate lyase but not C. albicans isocitrate lyase.
Authors: Keito Hiragi / Kazuya Nishio / Shu Moriyama / Tasuku Hamaguchi / Akira Mizoguchi / Koji Yonekura / Kazutoshi Tani / Tsunehiro Mizushima /
Abstract: In Saccharomyces cerevisiae, the glyoxylate cycle is controlled through the posttranslational regulation of its component enzymes, such as isocitrate lyase (ICL), which catalyzes the first unique ...In Saccharomyces cerevisiae, the glyoxylate cycle is controlled through the posttranslational regulation of its component enzymes, such as isocitrate lyase (ICL), which catalyzes the first unique step of the cycle. The ICL of S.cerevisiae (ScIcl1) is tagged for proteasomal degradation through ubiquitination by a multisubunit ubiquitin ligase (the glucose-induced degradation-deficient (GID) complex), whereas that of the pathogenic yeast Candida albicans (CaIcl1) escapes this process. However, the reason for the ubiquitin targeting specificity of the GID complex for ScIcl1 and not for CaIcl1 is unclear. To gain some insight into this, in this study, the crystal structures of apo ScIcl1 and CaIcl1 in complex with formate and the cryogenic electron microscopy structure of apo CaIcl1 were determined at a resolution of 2.3, 2.7, and 2.6 Å, respectively. A comparison of the various structures suggests that the orientation of N-terminal helix α1 in S.cerevisiae is likely key to repositioning of ubiquitination sites and contributes to the distinction found in C. albicans ubiquitin evasion mechanism. This finding gives us a better understanding of the molecular mechanism of ubiquitin-dependent ScIcl1 degradation and could serve as a theoretical basis for the research and development of anti-C. albicans drugs based on the concept of CaIcl1 ubiquitination.
History
DepositionMar 9, 2021-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ebf
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31053.png

Downloads & links

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Map

FileDownload / File: emd_31053.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 263.36 Å		0.82 Å/pix.
x 320 pix.
= 263.36 Å		0.82 Å/pix.
x 320 pix.
= 263.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.823 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0154 / Movie #1: 0.02
Minimum - Maximum-0.06679116 - 0.11573447
Average (Standard dev.)0.000013383141 (±0.0038372246)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8230.8230.823
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z263.360263.360263.360
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0670.1160.000

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Supplemental data

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Sample components

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Entire : Isocitrate lyase

EntireName: Isocitrate lyase
Components
  • Complex: Isocitrate lyase
    • Protein or peptide: Isocitrate lyase

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Supramolecule #1: Isocitrate lyase

SupramoleculeName: Isocitrate lyase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candida albicans (yeast)

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Macromolecule #1: Isocitrate lyase

MacromoleculeName: Isocitrate lyase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: isocitrate lyase
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 62.336523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHMPYT PIDIQKEEAD FQKEVAEIKK WWSEPRWRKT KRIYSAEDIA KKRGTLKINH PSSQQADKLF KLLEKHDADK TVSFTFGAL DPIHVAQMAK YLDSIYVSGW QCSSTASTSN EPSPDLADYP MDTVPNKVEH LWFAQLFHDR KQREERLTLS K EERAKTPY ...String:
HHHHHHMPYT PIDIQKEEAD FQKEVAEIKK WWSEPRWRKT KRIYSAEDIA KKRGTLKINH PSSQQADKLF KLLEKHDADK TVSFTFGAL DPIHVAQMAK YLDSIYVSGW QCSSTASTSN EPSPDLADYP MDTVPNKVEH LWFAQLFHDR KQREERLTLS K EERAKTPY IDFLRPIIAD ADTGHGGITA IIKLTKMFIE RGAAGIHIED QAPGTKKCGH MAGKVLVPVQ EHINRLVAIR AS ADIFGSN LLAVARTDSE AATLITSTID HRDHYFIIGA TNPEAGDLAA LMAEAESKGI YGNELAAIES EWTKKAGLKL FHE AVIDEI KNGNYSNKDA LIKKFTDKVN PLSHTSHKEA KKLAKELTGK DIYFNWDVAR AREGYYRYQG GTQCAVMRGR AFAP YADLI WMESALPDYA QAKEFADGVK AAVPDQWLAY NLSPSFNWNK AMPADEQETY IKRLGKLGYV WQFITLAGLH TTALA VDDF SNQYSQIGMK AYGQTVQQPE IEKGVEVVKH QKWSGATYID GLLKMVSGGV TSTAAMGQGV TEDQFKESKA KA

UniProtKB: Isocitrate lyase

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 278 K

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 42.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 179026
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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