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- EMDB-78898: Cryo EM structure of GTP cyclohydrolase 1 (FolE) from Mycobacteri... -

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Basic information

Entry
Database: EMDB / ID: EMD-78898
TitleCryo EM structure of GTP cyclohydrolase 1 (FolE) from Mycobacterium tuberculosis in complex with 8-oxo GTP
Map data
Sample
  • Complex: decamer of GTP cyclohydrolase 1
    • Protein or peptide: GTP cyclohydrolase 1
  • Ligand: ZINC ION
  • Ligand: 8-OXO-GUANOSINE-5'-TRIPHOSPHATE
KeywordsSSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / GTP cyclohydrolase 1 (FolE) / Mycobacterium tuberculosis / HYDROLASE
Function / homology
Function and homology information


GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrobiopterin biosynthetic process / tetrahydrofolate biosynthetic process / one-carbon metabolic 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 speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsLiu L / Lovell S / Hammons AM / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD036339 United States
CitationJournal: To be published
Title: Cryo EM structure of GTP cyclohydrolase 1 (FolE) from Mycobacterium tuberculosis in complex with 8-oxo GTP
Authors: Liu L / Lovell S / Hammons AM
History
DepositionSep 1, 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_78898.png

Downloads & links

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Map

FileDownload / File: emd_78898.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 200 pix.
= 236. Å		1.18 Å/pix.
x 200 pix.
= 236. Å		1.18 Å/pix.
x 200 pix.
= 236. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.174
Minimum - Maximum-0.1881827 - 0.5173602
Average (Standard dev.)-0.000018358945 (±0.02315453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 235.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_78898_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_78898_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_78898_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 : decamer of GTP cyclohydrolase 1

EntireName: decamer of GTP cyclohydrolase 1
Components
  • Complex: decamer of GTP cyclohydrolase 1
    • Protein or peptide: GTP cyclohydrolase 1
  • Ligand: ZINC ION
  • Ligand: 8-OXO-GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: decamer of GTP cyclohydrolase 1

SupramoleculeName: decamer of GTP cyclohydrolase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 247 KDa

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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: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 24.717246 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAHHHHHHMG TLEAQTQGPG SMSQLDSRSA SARIRVFDQQ RAEAAVRELL YAIGEDPDRD GLVATPSRVA RSYREMFAGL YTDPDSVLN TMFDEDHDEL VLVKEIPMYS TCEHHLVAFH GVAHVGYIPG DDGRVTGLSK IARLVDLYAK RPQVQERLTS Q IADALMKK ...String:
MAHHHHHHMG TLEAQTQGPG SMSQLDSRSA SARIRVFDQQ RAEAAVRELL YAIGEDPDRD GLVATPSRVA RSYREMFAGL YTDPDSVLN TMFDEDHDEL VLVKEIPMYS TCEHHLVAFH GVAHVGYIPG DDGRVTGLSK IARLVDLYAK RPQVQERLTS Q IADALMKK LDPRGVIVVI EAEHLCMAMR GVRKPGSVTT TSAVRGLFKT NAASRAEALD LILRK

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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration2.8 mg/mL
BufferpH: 7
Details: 25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide
Sugar embeddingMaterial: VITREOUS ICE
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 1 sec. / Pretreatment - Pressure: 0.005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 15378 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

DetailsThe selected images were high-pass filtered and normalized
Particle selectionNumber selected: 24782213
CTF correctionSoftware - Name: cryoSPARC (ver. 5.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

11yz

Final reconstructionNumber classes used: 81 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 990760
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 200 / Software - Name: cryoSPARC (ver. 5.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

11yz


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.12)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-38kz:
Cryo EM structure of GTP cyclohydrolase 1 (FolE) from Mycobacterium tuberculosis in complex with 8-oxo GTP

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