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- EMDB-15052: CryoEM structure of DHS-eIF5A1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-15052
TitleCryoEM structure of DHS-eIF5A1 complex
Map datamain map
Sample
  • Complex: Complex of human DHS-eIF5A
    • Protein or peptide: Deoxyhypusine synthase
    • Protein or peptide: Deoxyhypusine synthase
    • Protein or peptide: Eukaryotic translation initiation factor 5A
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: SPERMIDINE
Function / homology
Function and homology information


deoxyhypusine synthase / deoxyhypusine synthase activity / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / spermidine metabolic process / spermidine catabolic process / positive regulation of translational termination / positive regulation of translational elongation / translation elongation factor activity / positive regulation of T cell proliferation ...deoxyhypusine synthase / deoxyhypusine synthase activity / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / spermidine metabolic process / spermidine catabolic process / positive regulation of translational termination / positive regulation of translational elongation / translation elongation factor activity / positive regulation of T cell proliferation / translation initiation factor activity / ribosome binding / glucose homeostasis / translation / positive regulation of cell population proliferation / endoplasmic reticulum membrane / RNA binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / DHS-like NAD/FAD-binding domain superfamily ...Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / DHS-like NAD/FAD-binding domain superfamily / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Eukaryotic translation initiation factor 5A / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWator E / Wilk P / Biela AP / Rawski M / Grudnik P
Funding support Poland, 2 items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2019/33/B/NZ1/01839 Poland
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of human eIF5A-DHS complex reveals the molecular basis of hypusination-associated neurodegenerative disorders.
Authors: Elżbieta Wątor / Piotr Wilk / Artur Biela / Michał Rawski / Krzysztof M Zak / Wieland Steinchen / Gert Bange / Sebastian Glatt / Przemysław Grudnik /
Abstract: Hypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The ...Hypusination is a unique post-translational modification of the eukaryotic translation factor 5A (eIF5A) that is essential for overcoming ribosome stalling at polyproline sequence stretches. The initial step of hypusination, the formation of deoxyhypusine, is catalyzed by deoxyhypusine synthase (DHS), however, the molecular details of the DHS-mediated reaction remained elusive. Recently, patient-derived variants of DHS and eIF5A have been linked to rare neurodevelopmental disorders. Here, we present the cryo-EM structure of the human eIF5A-DHS complex at 2.8 Å resolution and a crystal structure of DHS trapped in the key reaction transition state. Furthermore, we show that disease-associated DHS variants influence the complex formation and hypusination efficiency. Hence, our work dissects the molecular details of the deoxyhypusine synthesis reaction and reveals how clinically-relevant mutations affect this crucial cellular process.
History
DepositionMay 27, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateApr 5, 2023-
Current statusApr 5, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15052.png

Downloads & links

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Map

FileDownload / File: emd_15052.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.244
Minimum - Maximum-0.7249341 - 1.2853668
Average (Standard dev.)0.0019006045 (±0.048705503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_15052_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_15052_half_map_2.map
Annotationhalf map B
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 human DHS-eIF5A

EntireName: Complex of human DHS-eIF5A
Components
  • Complex: Complex of human DHS-eIF5A
    • Protein or peptide: Deoxyhypusine synthase
    • Protein or peptide: Deoxyhypusine synthase
    • Protein or peptide: Eukaryotic translation initiation factor 5A
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: SPERMIDINE

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Supramolecule #1: Complex of human DHS-eIF5A

SupramoleculeName: Complex of human DHS-eIF5A / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 / Details: monomer of eIF5A bound to homotetramer DHS.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 181.687 KDa

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Macromolecule #1: Deoxyhypusine synthase

MacromoleculeName: Deoxyhypusine synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: deoxyhypusine synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.098461 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMEGSLERE APAGALAAVL KHSSTLPPES TQVRGYDFNR GVNYRALLEA FGTTGFQATN FGRAVQQVNA MIEKKLEPLS QDEDQHADL TQSRRPLTSC TIFLGYTSNL ISSGIRETIR YLVQHNMVDV LVTTAGGVEE DLIKCLAPTY LGEFSLRGKE L RENGINRI ...String:
GSMEGSLERE APAGALAAVL KHSSTLPPES TQVRGYDFNR GVNYRALLEA FGTTGFQATN FGRAVQQVNA MIEKKLEPLS QDEDQHADL TQSRRPLTSC TIFLGYTSNL ISSGIRETIR YLVQHNMVDV LVTTAGGVEE DLIKCLAPTY LGEFSLRGKE L RENGINRI GNLLVPNENY CKFEDWLMPI LDQMVMEQNT EGVKWTPSKM IARLGKEINN PESVYYWAQK NHIPVFSPAL TD GSLGDMI FFHSYKNPGL VLDIVEDLRL INTQAIFAKC TGMIILGGGV VKHHIANANL MRNGADYAVY INTAQEFDGS DSG ARPDEA VSWGAIRVDA QPVKVYADAS LVFPLLVAET FAQKMDAFMH EKNED

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Macromolecule #2: Deoxyhypusine synthase

MacromoleculeName: Deoxyhypusine synthase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: deoxyhypusine synthase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.130527 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMEGSLERE APAGALAAVL KHSSTLPPES TQVRGYDFNR GVNYRALLEA FGTTGFQATN FGRAVQQVNA MIEKKLEPLS QDEDQHADL TQSRRPLTSC TIFLGYTSNL ISSGIRETIR YLVQHNMVDV LVTTAGGVEE DLIKCLAPTY LGEFSLRGKE L RENGINRI ...String:
GSMEGSLERE APAGALAAVL KHSSTLPPES TQVRGYDFNR GVNYRALLEA FGTTGFQATN FGRAVQQVNA MIEKKLEPLS QDEDQHADL TQSRRPLTSC TIFLGYTSNL ISSGIRETIR YLVQHNMVDV LVTTAGGVEE DLIKCLAPTY LGEFSLRGKE L RENGINRI GNLLVPNENY (CSS)KFEDWLMPI LDQMVMEQNT EGVKWTPSKM IARLGKEINN PESVYYWAQK NHIPVFSP A LTDGSLGDMI FFHSYKNPGL VLDIVEDLRL INTQAIFAKC TGMIILGGGV VKHHIANANL MRNGADYAVY INTAQEFDG SDSGARPDEA VSWGAIRVDA QPVKVYADAS LVFPLLVAET FAQKMDAFMH EKNED

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Macromolecule #3: Eukaryotic translation initiation factor 5A

MacromoleculeName: Eukaryotic translation initiation factor 5A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.998395 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSMADDLDFE TGDAGASATF PMQCSALRKN GFVVLKGRPC KIVEMSTSKT GKHGHAKVHL VGIDIFTGKK YEDICPSTHN MDVPNIKRN DFQLIGIQDG YLSLLQDSGE VREDLRLPEG DLGKEIEQKY DCGEEILITV LSAMTEEAAV AIKAMAK

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Macromolecule #4: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

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Macromolecule #5: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 5 / Number of copies: 3 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE / Spermidine

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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

Concentration0.12 mg/mL
BufferpH: 9.3
Component:
ConcentrationFormulaName
0.2 MNaOH/Glycineglycine buffer
0.2 MNaClSodium chloridesodium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 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 / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1277576 / Details: autopicked particles
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5 / Avg.num./class: 100000 / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 490582
Detailsselected images were normalized and low-pass filtered
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6xxj

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8a0e:
CryoEM structure of DHS-eIF5A1 complex

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