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- EMDB-64214: Complex of GTP cyclohydrolase with GTP -

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Basic information

Entry
Database: EMDB / ID: EMD-64214
TitleComplex of GTP cyclohydrolase with GTP
Map data
Sample
  • Complex: Complex of GTP cyclohydrolase with GTP
    • Protein or peptide: GTP cyclohydrolase 1
  • Ligand: ZINC ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: water
KeywordsGTP cyclohydrolase GTP HYDROLASE BIOSYNTHETIC PROTEIN / BIOSYNTHETIC PROTEIN
Function / homology:
Function and homology information
Biological speciesStreptomyces mobaraensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.01 Å
AuthorsWang YL / Hsu NS / Li TL
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: To Be Published
Title: Biosynthesis of 5-azacytidine
Authors: Wang YL / Hsu NS / Li TL
History
DepositionApr 17, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64214.png

Downloads & links

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Map

FileDownload / File: emd_64214.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-3.5916052 - 6.2786217
Average (Standard dev.)-0.0017308579 (±0.15186206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64214_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_64214_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 : Complex of GTP cyclohydrolase with GTP

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

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Supramolecule #1: Complex of GTP cyclohydrolase with GTP

SupramoleculeName: Complex of GTP cyclohydrolase with GTP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptomyces mobaraensis (bacteria) / Strain: ATCC 27441

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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: Streptomyces mobaraensis (bacteria)
Molecular weightTheoretical: 22.322334 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MTIAEWLQEN VTTDKRALDW YTEPECEPRI VRAYKELLSG YEVDTSKILK TTVLVKGDHQ GVVRVRDIN YYSICAHHFL PFYGKVDITY VPGDRILGLG KFPRLVQAFS KRFQIQEHLV KDIAEEIMSS GGARAVRVES S GRHMCMCS ...String:
MGSSHHHHHH SSGLVPRGSH MTIAEWLQEN VTTDKRALDW YTEPECEPRI VRAYKELLSG YEVDTSKILK TTVLVKGDHQ GVVRVRDIN YYSICAHHFL PFYGKVDITY VPGDRILGLG KFPRLVQAFS KRFQIQEHLV KDIAEEIMSS GGARAVRVES S GRHMCMCS RGPSDQTVIT DTTYVTGDTE LLTAYGQQR

UniProtKB: UNIPROTKB: A0A7X1IDJ8

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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: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 10 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 135 / 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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 195382
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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