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- PDB-37xd: Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans a... -

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Basic information

Entry
Database: PDB / ID: 37xd
TitleCryo-EM Structure of GTP Cyclohydrolase I from Candida albicans at 2.6 A
ComponentsGTP cyclohydrolase 1
KeywordsANTIFUNGAL PROTEIN / GTP Cyclohydrolase I / Candida albicans / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsOluwarotimi, E.A. / Guo, Y. / Borek, D. / Mesecar, A.D. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
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
Authors: Oluwarotimi, E.A. / Guo, Y. / Borek, D. / Mesecar, A.D. / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionAug 11, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP cyclohydrolase 1
B: GTP cyclohydrolase 1
C: GTP cyclohydrolase 1
D: GTP cyclohydrolase 1
E: GTP cyclohydrolase 1
F: GTP cyclohydrolase 1
G: GTP cyclohydrolase 1
H: GTP cyclohydrolase 1
I: GTP cyclohydrolase 1
J: GTP cyclohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,98620
Polymers217,33210
Non-polymers65410
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
GTP cyclohydrolase 1 / GTP cyclohydrolase I


Mass: 21733.164 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CAWG_04839 / Production host: Escherichia coli (E. coli) / References: UniProt: C4YRY1, GTP cyclohydrolase I
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans at 2.62 A
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 31.6 kDa/nm / Experimental value: NO
Source (natural)Organism: Candida albicans (yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationCryogen name: ETHANE

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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: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
7UCSF ChimeraX1.12model fitting
12cryoSPARC3D reconstruction
13PHENIX2.2_6143model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 204567 / Symmetry type: POINT
RefinementHighest resolution: 2.62 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215420
ELECTRON MICROSCOPYf_angle_d0.60420690
ELECTRON MICROSCOPYf_dihedral_angle_d3.9942110
ELECTRON MICROSCOPYf_chiral_restr0.0482340
ELECTRON MICROSCOPYf_plane_restr0.0032650

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