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- EMDB-24540: Structure of ligand-free ALDH1L1 (10-formyltetrahydrofolate dehyd... -

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Basic information

Entry
Database: EMDB / ID: EMD-24540
TitleStructure of ligand-free ALDH1L1 (10-formyltetrahydrofolate dehydrogenase)
Map dataPost-processed map
Sample
  • Complex: ligand-free ALDH1L1
    • Protein or peptide: Cytosolic 10-formyltetrahydrofolate dehydrogenase
  • Ligand: 4'-PHOSPHOPANTETHEINE
Function / homology
Function and homology information


Metabolism of folate and pterines / aldehyde dehydrogenase (NADP+) activity / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / NADPH regeneration / aldehyde dehydrogenase (NAD+) activity / folic acid metabolic process / tetrahydrofolate biosynthetic process ...Metabolism of folate and pterines / aldehyde dehydrogenase (NADP+) activity / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / NADPH regeneration / aldehyde dehydrogenase (NAD+) activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / protein-containing complex binding / protein-containing complex / 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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Cytosolic 10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsTsybovsky Y / Sereda V / Golczak M / Krupenko NI / Krupenko SA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK54388 United States
CitationJournal: Commun Biol / Year: 2022
Title: Structure of putative tumor suppressor ALDH1L1.
Authors: Yaroslav Tsybovsky / Valentin Sereda / Marcin Golczak / Natalia I Krupenko / Sergey A Krupenko /
Abstract: Putative tumor suppressor ALDH1L1, the product of natural fusion of three unrelated genes, regulates folate metabolism by catalyzing NADP-dependent conversion of 10-formyltetrahydrofolate to ...Putative tumor suppressor ALDH1L1, the product of natural fusion of three unrelated genes, regulates folate metabolism by catalyzing NADP-dependent conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO. Cryo-EM structures of tetrameric rat ALDH1L1 revealed the architecture and functional domain interactions of this complex enzyme. Highly mobile N-terminal domains, which remove formyl from 10-formyltetrahydrofolate, undergo multiple transient inter-domain interactions. The C-terminal aldehyde dehydrogenase domains, which convert formyl to CO, form unusually large interfaces with the intermediate domains, homologs of acyl/peptidyl carrier proteins (A/PCPs), which transfer the formyl group between the catalytic domains. The 4'-phosphopantetheine arm of the intermediate domain is fully extended and reaches deep into the catalytic pocket of the C-terminal domain. Remarkably, the tetrameric state of ALDH1L1 is indispensable for catalysis because the intermediate domain transfers formyl between the catalytic domains of different protomers. These findings emphasize the versatility of A/PCPs in complex, highly dynamic enzymatic systems.
History
DepositionJul 26, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateFeb 2, 2022-
Current statusFeb 2, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-7rlt
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rlt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24540.png

Downloads & links

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Map

FileDownload / File: emd_24540.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 160 pix.
= 211.2 Å		1.32 Å/pix.
x 160 pix.
= 211.2 Å		1.32 Å/pix.
x 160 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.13307178 - 0.20036858
Average (Standard dev.)0.000535989 (±0.008558723)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 211.20001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z211.200211.200211.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1330.2000.001

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Supplemental data

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Mask #1

Fileemd_24540_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refined map before post-processing

Fileemd_24540_additional_1.map
AnnotationRefined map before post-processing
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_24540_half_map_1.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1

Fileemd_24540_half_map_2.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ligand-free ALDH1L1

EntireName: ligand-free ALDH1L1
Components
  • Complex: ligand-free ALDH1L1
    • Protein or peptide: Cytosolic 10-formyltetrahydrofolate dehydrogenase
  • Ligand: 4'-PHOSPHOPANTETHEINE

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Supramolecule #1: ligand-free ALDH1L1

SupramoleculeName: ligand-free ALDH1L1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 395 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: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 98.985055 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKIAVIGQSL FGQEVYCQLR KEGHEVVGVF TIPDKDGKAD PLGLEAEKDG VPVFKFPRWR ARGQALPEVV AKYQALGAEL NVLPFCSQF IPMEVINAPR HGSIIYHPSL LPRHRGASAI NWTLIHGDKK GGFTIFWADD GLDTGDLLLQ KECEVLPDDT V STLYNRFL ...String:
MKIAVIGQSL FGQEVYCQLR KEGHEVVGVF TIPDKDGKAD PLGLEAEKDG VPVFKFPRWR ARGQALPEVV AKYQALGAEL NVLPFCSQF IPMEVINAPR HGSIIYHPSL LPRHRGASAI NWTLIHGDKK GGFTIFWADD GLDTGDLLLQ KECEVLPDDT V STLYNRFL FPEGIKGMVQ AVRLIAEGTA PRCPQSEEGA TYEGIQKKET AKINWDQPAE AIHNWIRGND KVPGAWTEAC GQ KLTFFNS TLNTSGLSTQ GEALPIPGAH RPGVVTKAGL ILFGNDDRML LVKNIQLEDG KMMPASQFFK GSASSDLELT EAE LATAEA VRSSWMRILP NVPEVEDSTD FFKSGAASVD VVRLVEEVKE LCDGLELENE DVYMATTFRG FIQLLVRKLR GEDD ESECV INYVEKAVNK LTLQMPYQLF IGGEFVDAEG SKTYNTINPT DGSVICQVSL AQVSDVDKAV AAAKEAFENG LWGKI NARD RGRLLYRLAD VMEQHQEELA TIEALDAGAV YTLALKTHVG MSIQTFRYFA GWCDKIQGAT IPINQARPNR NLTLTK KEP VGVCGIVIPW NYPLMMLSWK TAACLAAGNT VVIKPAQVTP LTALKFAELT LKAGIPKGVV NILPGSGSLV GQRLSDH PD VRKIGFTGST EVGKHIMKSC ALSNVKKVSL ELGGKSPLII FADCDLNKAV QMGMSSVFFN KGENCIAAGR LFVEESIH N QFVQKVVEEV EKMKIGNPLE RDTNHGPQNH EAHLRKLVEY CQRGVKEGAT LVCGGNQVPR PGFFFQPTVF TDVEDHMYI AKEESFGPIM IISRFADGDV DAVLSRANAT EFGLASGVFT RDINKALYVS DKLQAGTVFI NTYNKTDVAA PFGGFKQSGF GKDLGEAAL NEYLRIKTVT FEY

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Macromolecule #2: 4'-PHOSPHOPANTETHEINE

MacromoleculeName: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: PNS
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE

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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

Concentration0.4 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

2o2p

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 86276
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2o2p

RefinementProtocol: BACKBONE TRACE
Output model

PDB-7rlt:
Structure of ligand-free ALDH1L1 (10-formyltetrahydrofolate dehydrogenase)

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