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- EMDB-78820: Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans b... -

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Basic information

Entry
Database: EMDB / ID: EMD-78820
TitleCryo-EM Structure of GTP Cyclohydrolase I from Candida albicans bound to 7-Deaza GTP and BH2 at 1.96 A
Map data
Sample
  • Complex: Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans bound to 7-Deaza GTP and BH2 at 1.96 A
    • Protein or peptide: GTP cyclohydrolase 1
  • Ligand: 7,8-DIHYDROBIOPTERIN
  • Ligand: ZINC ION
  • Ligand: 7-deaza-GTP
  • Ligand: water
Keywordsantifungal / 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: 1.95 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 7-Deaza GTP and BH2 at 1.96 A
Authors: Oluwarotimi EA / Guo Y / Vago F / Klose T / Borek D / Mesecar AD / Center for Structural Biology of Infectious Diseases (CSBID)
History
DepositionAug 27, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78820.png

Downloads & links

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Map

FileDownload / File: emd_78820.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: 0.00391
Minimum - Maximum-0.044244256 - 0.21630508
Average (Standard dev.)-0.000055824814 (±0.004494288)
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_78820_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_78820_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 : Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans b...

EntireName: Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans bound to 7-Deaza GTP and BH2 at 1.96 A
Components
  • Complex: Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans bound to 7-Deaza GTP and BH2 at 1.96 A
    • Protein or peptide: GTP cyclohydrolase 1
  • Ligand: 7,8-DIHYDROBIOPTERIN
  • Ligand: ZINC ION
  • Ligand: 7-deaza-GTP
  • Ligand: water

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Supramolecule #1: Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans b...

SupramoleculeName: Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans bound to 7-Deaza GTP and BH2 at 1.96 A
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: 7,8-DIHYDROBIOPTERIN

MacromoleculeName: 7,8-DIHYDROBIOPTERIN / type: ligand / ID: 2 / Number of copies: 10 / Formula: HBI
Molecular weightTheoretical: 239.231 Da
Chemical component information

ChemComp-HBI:
7,8-DIHYDROBIOPTERIN

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: 7-deaza-GTP

MacromoleculeName: 7-deaza-GTP / type: ligand / ID: 4 / Number of copies: 10 / Formula: QBQ
Molecular weightTheoretical: 522.192 Da
Chemical component information

ChemComp-QBQ:
7-deaza-GTP

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 282 / 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: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 400 / Support film - Material: GRAPHENE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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: 300.0 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
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: 1.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 408114
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-38hm:
Cryo-EM Structure of GTP Cyclohydrolase I from Candida albicans bound to 7-Deaza GTP and BH2 at 1.96 A

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