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- EMDB-24547: Structure of ALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in... -

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Basic information

Entry
Database: EMDB / ID: EMD-24547
TitleStructure of ALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in complex with NADP
Map dataALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in complex with NADP
Sample
  • Complex: ALDH1L1 in complex with NADP
    • Protein or peptide: Cytosolic 10-formyltetrahydrofolate dehydrogenase
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: 4'-PHOSPHOPANTETHEINEPhosphopantetheine
  • Ligand: water
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 / bile acid signaling pathway / folic acid metabolic 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 / bile acid signaling pathway / 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, N-terminal / Aldehyde dehydrogenase, C-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: 2.9 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: 0.02
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  • Surface view colored by radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-7rlu
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rlu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24547.png

Downloads & links

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Map

FileDownload / File: emd_24547.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in complex with NADP
Voxel sizeX=Y=Z: 0.76 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.113454394 - 0.14258367
Average (Standard dev.)0.00019174351 (±0.005132242)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 212.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.760.760.76
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z212.800212.800212.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1130.1430.000

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Supplemental data

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Mask #1

Fileemd_24547_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: ALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in complex with NADP...

Fileemd_24547_additional_1.map
AnnotationALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in complex with NADP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in complex with NADP...

Fileemd_24547_half_map_1.map
AnnotationALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in complex with NADP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in complex with NADP...

Fileemd_24547_half_map_2.map
AnnotationALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in complex with NADP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ALDH1L1 in complex with NADP

EntireName: ALDH1L1 in complex with NADP
Components
  • Complex: ALDH1L1 in complex with NADP
    • Protein or peptide: Cytosolic 10-formyltetrahydrofolate dehydrogenase
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: 4'-PHOSPHOPANTETHEINEPhosphopantetheine
  • Ligand: water

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Supramolecule #1: ALDH1L1 in complex with NADP

SupramoleculeName: ALDH1L1 in complex with NADP / 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: 98.957047 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 GSASSSLELT 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: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

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Macromolecule #3: 4'-PHOSPHOPANTETHEINE

MacromoleculeName: 4'-PHOSPHOPANTETHEINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: PNS
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PNS:
4'-PHOSPHOPANTETHEINE / Phosphopantetheine

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 28 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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

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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
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:

2o2q

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 202398
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-7rlu:
Structure of ALDH1L1 (10-formyltetrahydrofolate dehydrogenase) in complex with NADP

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