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- EMDB-33872: Human Cytosolic 10-formyltetrahydrofolate dehydrogenase and Gossy... -

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Basic information

Entry
Database: EMDB / ID: EMD-33872
TitleHuman Cytosolic 10-formyltetrahydrofolate dehydrogenase and Gossypol complex
Map data
Sample
  • Complex: Human Cytosolic 10-formyltetrahydrofolate dehydrogenase and Gossypol complex
    • Protein or peptide: Cytosolic 10-formyltetrahydrofolate dehydrogenase
  • Ligand: Gossypol
KeywordsCytosolic 10-formyltetrahydrofolate dehydrogenase / Aldehyde dehydrogenase family 1 member L1 / inhibitor / Gossypol / OXIDOREDUCTASE
Function / homology
Function and homology information


formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / NADPH regeneration / Metabolism of folate and pterines / aldehyde dehydrogenase (NAD+) activity / biosynthetic process / one-carbon metabolic process / extracellular exosome / cytosol
Similarity search - Function
10-formyltetrahydrofolate dehydrogenase / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily ...10-formyltetrahydrofolate dehydrogenase / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Cytosolic 10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.31 Å
AuthorsHan CW / Lee HN / Jeong MS / Jang SB
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Human Cytosolic 10-formyltetrahydrofolate dehydrogenase and Gossypol complex
Authors: Han CW / Lee HN / Jeong MS / Jang SB
History
DepositionJul 20, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33872.png

Downloads & links

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Map

FileDownload / File: emd_33872.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.9663 Å
Density
Contour LevelBy AUTHOR: 0.141
Minimum - Maximum-1.7791698 - 2.9586198
Average (Standard dev.)-0.00049516186 (±0.07286049)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 503.3728 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_33872_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33872_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33872_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Human Cytosolic 10-formyltetrahydrofolate dehydrogenase and Gossy...

EntireName: Human Cytosolic 10-formyltetrahydrofolate dehydrogenase and Gossypol complex
Components
  • Complex: Human Cytosolic 10-formyltetrahydrofolate dehydrogenase and Gossypol complex
    • Protein or peptide: Cytosolic 10-formyltetrahydrofolate dehydrogenase
  • Ligand: Gossypol

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Supramolecule #1: Human Cytosolic 10-formyltetrahydrofolate dehydrogenase and Gossy...

SupramoleculeName: Human Cytosolic 10-formyltetrahydrofolate dehydrogenase and Gossypol complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Protein (Human Cytosolic 10-formyltetrahydrofolate dehydrogenase) and chemical (Gossypol) complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 223 KDa

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Macromolecule #1: Cytosolic 10-formyltetrahydrofolate dehydrogenase

MacromoleculeName: Cytosolic 10-formyltetrahydrofolate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: formyltetrahydrofolate dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.439246 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SIDYVEMAVN KRTVRMPHQL FIGGEFVDAE GAKTSETINP TDGSVICQVS LAQVTDVDKA VAAAKDAFEN GRWGKISARD RGRLMYRLA DLMEQHQEEL ATIEALDAGA VYTLALKTHV GMSIQTFRYF AGWCDKIQGS TIPINQARPN RNLTLTRKEP V GVCGIIIP ...String:
SIDYVEMAVN KRTVRMPHQL FIGGEFVDAE GAKTSETINP TDGSVICQVS LAQVTDVDKA VAAAKDAFEN GRWGKISARD RGRLMYRLA DLMEQHQEEL ATIEALDAGA VYTLALKTHV GMSIQTFRYF AGWCDKIQGS TIPINQARPN RNLTLTRKEP V GVCGIIIP WNYPLMMLSW KTAACLAAGN TVVIKPAQVT PLTALKFAEL TLKAGIPKGV VNVLPGSGSL VGQRLSDHPD VR KIGFTGS TEVGKHIMKS CAISNVKKVS LELGGKSPLI IFADCDLNKA VQMGMSSVFF NKGENCIAAG RLFVEDSIHD EFV RRVVEE VRKMKVGNPL DRDTDHGPQN HHAHLVKLME YCQHGVKEGA TLVCGGNQVP RPGFFFEPTV FTDVEDHMFI AKEE SFGPV MIISRFADGD LDAVLSRANA TEFGLASGVF TRDINKALYV SDKLQAGTVF VNTYNKTDVA APFGGFKQSG FGKDL GEAA LNEYLRVKTV TFEY

UniProtKB: Cytosolic 10-formyltetrahydrofolate dehydrogenase

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Macromolecule #2: Gossypol

MacromoleculeName: Gossypol / type: ligand / ID: 2 / Number of copies: 1 / Formula: GO3
Molecular weightTheoretical: 518.554 Da
Chemical component information

ChemComp-GO3:
Gossypol

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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: 7.8
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 54.56 sec. / Average electron dose: 39.55 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4go0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 396292
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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