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- EMDB-78634: Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans b... -

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Basic information

Entry
Database: EMDB / ID: EMD-78634
TitleCryo-EM Structure of GTP Cyclohydrolase I from Candida albicans bound to 8-oxo GTP at 1.74 A
Map data
Sample
  • Complex: GTP Cyclohydrolase I bound to 8-oxo GTP
    • Protein or peptide: GTP cyclohydrolase 1
  • Ligand: ZINC ION
  • Ligand: 8-OXO-GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: water
KeywordsGTP Cyclohydrolase I / Candida albicans / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / ANTIFUNGAL PROTEIN
Function / homology
Function and homology information


GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrobiopterin biosynthetic process / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / GTP binding / zinc ion binding / cytoplasm
Similarity search - Function
GTP cyclohydrolase I signature 2. / GTP cyclohydrolase I / GTP cyclohydrolase I, conserved site / GTP cyclohydrolase I domain / GTP cyclohydrolase I, N-terminal domain / GTP cyclohydrolase I / GTP cyclohydrolase I signature 1. / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Domain/homology
GTP cyclohydrolase 1
Similarity search - Component
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.74 Å
AuthorsOluwarotimi EA / Guo Y / Vago F / Klose T / Borek D / Mesecar AD / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: To Be Published
Title: Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans bound to 8-oxo GTP at 1.74 A
Authors: Oluwarotimi EA / Guo Y / Vago F / Klose T / Borek D / Mesecar AD / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionAug 12, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78634.png

Downloads & links

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Map

FileDownload / File: emd_78634.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.55 Å/pix.
x 480 pix.
= 263.04 Å		0.55 Å/pix.
x 480 pix.
= 263.04 Å		0.55 Å/pix.
x 480 pix.
= 263.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.548 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00495
Minimum - Maximum-0.045637164 - 0.2364564
Average (Standard dev.)-0.00009786133 (±0.004899369)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 263.03998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_78634_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_78634_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 : GTP Cyclohydrolase I bound to 8-oxo GTP

EntireName: GTP Cyclohydrolase I bound to 8-oxo GTP
Components
  • Complex: GTP Cyclohydrolase I bound to 8-oxo GTP
    • Protein or peptide: GTP cyclohydrolase 1
  • Ligand: ZINC ION
  • Ligand: 8-OXO-GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: water

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Supramolecule #1: GTP Cyclohydrolase I bound to 8-oxo GTP

SupramoleculeName: GTP Cyclohydrolase I bound to 8-oxo GTP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Candida albicans (yeast)

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Macromolecule #1: GTP cyclohydrolase 1

MacromoleculeName: GTP cyclohydrolase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO / EC number: GTP cyclohydrolase I
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 31.677264 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNPSHNPKH HLREEDSNGT QDGPKSTVPI KRSKLVGSSN LVSPNFLPRD LIETPLQTRA ASPLTLNPPI DSDGLSWPSQ GARLRIEQT SEEAKAREER IASAVKVILE ELGEDTSREG LLETPERYAR AMLYFTKGYE DNIRDVIKRA VFEEDHDEMV I VRDIEIYS ...String:
MSNPSHNPKH HLREEDSNGT QDGPKSTVPI KRSKLVGSSN LVSPNFLPRD LIETPLQTRA ASPLTLNPPI DSDGLSWPSQ GARLRIEQT SEEAKAREER IASAVKVILE ELGEDTSREG LLETPERYAR AMLYFTKGYE DNIRDVIKRA VFEEDHDEMV I VRDIEIYS LCEHHLVPFF GKAHIAYIPN KRVLGLSKLA RLAEMYSRRF QVQERLTKQI AMALSEILKP RGVAVVIEAT HM CMVSRGV QKTGSSTTTS CMLGCFRDQQ KTREEFLTLL GRK

UniProtKB: GTP cyclohydrolase 1

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: 8-OXO-GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 8-OXO-GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 10 / Formula: 8GT
Molecular weightTheoretical: 539.18 Da
Chemical component information

ChemComp-8GT:
8-OXO-GUANOSINE-5'-TRIPHOSPHATE

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 673 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
Component:
ConcentrationFormulaName
25.0 mMTrisTris(hydroxymethyl)aminomethane
150.0 mMNaClSodium Chloride
1.0 mMTCEPTris(2-carboxyethyl)phosphine
GridModel: EMS Lacey Carbon / Material: GOLD / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 1.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 485973
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / 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
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-37ya:
Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans bound to 8-oxo GTP at 1.74 A

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