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- EMDB-27871: CryoEM structure of yeast Arginyltransferase 1 (ATE1) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-27871
TitleCryoEM structure of yeast Arginyltransferase 1 (ATE1)
Map data
Sample
  • Complex: apo form of yeast Arginyltransferase 1
    • Protein or peptide: Arginyl-tRNA--protein transferase 1
  • Ligand: ZINC ION
Function / homology
Function and homology information


protein arginylation / arginyltransferase / arginyl-tRNA--protein transferase activity / cytoplasm
Similarity search - Function
N-end aminoacyl transferase, N-terminal / N-end rule aminoacyl transferase, C-terminal / N-end rule aminoacyl transferase / Arginine-tRNA-protein transferase, N terminus / Arginine-tRNA-protein transferase, C terminus / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Arginyl-tRNA--protein transferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHuang W / Zhang Y / Taylor DJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133841 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA241301 United States
CitationJournal: Nat Commun / Year: 2023
Title: The structural basis of tRNA recognition by arginyl-tRNA-protein transferase
Authors: Abeywansha T / Huang W / Ye X / Nawrocki A / Lan X / Jankowsky E / Taylor DJ / Zhang Y
History
DepositionAug 17, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateApr 26, 2023-
Current statusApr 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27871.png

Downloads & links

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Map

FileDownload / File: emd_27871.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8726 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.34355107 - 0.51378316
Average (Standard dev.)1.1341188e-05 (±0.010643962)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 223.3856 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27871_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_27871_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 : apo form of yeast Arginyltransferase 1

EntireName: apo form of yeast Arginyltransferase 1
Components
  • Complex: apo form of yeast Arginyltransferase 1
    • Protein or peptide: Arginyl-tRNA--protein transferase 1
  • Ligand: ZINC ION

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Supramolecule #1: apo form of yeast Arginyltransferase 1

SupramoleculeName: apo form of yeast Arginyltransferase 1 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Arginyl-tRNA--protein transferase 1

MacromoleculeName: Arginyl-tRNA--protein transferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: arginyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 58.001277 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDRFVIWAP SMHNEPAAKC GYCHGNKGGN MDQLFALDSW AHRYMNKMDV VKIENCTIGS FVEHMDVATY DRMCNMGFRR SGKFLYKVD PLRNCCRLYT IRTAPQELNM TKELKKCISR FATRITSEDY CPAAVASSDF VGKIVNAEMN SKTFYTRFEP A LYSEEKYH ...String:
MSDRFVIWAP SMHNEPAAKC GYCHGNKGGN MDQLFALDSW AHRYMNKMDV VKIENCTIGS FVEHMDVATY DRMCNMGFRR SGKFLYKVD PLRNCCRLYT IRTAPQELNM TKELKKCISR FATRITSEDY CPAAVASSDF VGKIVNAEMN SKTFYTRFEP A LYSEEKYH LFVKYQEKVH QDYNNSPKSF KRFLCDTPFG PEAVLGTQES WEQLNNWQRM KPGEKLKHMG PVHECYYYEG KL IAITVSD ILPSGISSVY FIWDPDYSKW SLGKLSALRD LAIIQRTNLQ YYYLGYYIED CPKMNYKANY GAEVLDVCHS KYI PLKPIQ DMISRGKLFV IGEEETKVTK ELYLVDSETG RGEGFPTDNV VKYKNIAEEI YGVGGCAFKS ANESALELKE LYGI PYEEE DLDTIYHLKE HNGHAPNGIP NVVPGLLPLW ELLDIMQSGK ITDLEGRLFL FEIETEGIRP LINFYSEPPN VKKRI CDVI RLFGFETCMK AVILYSEQM

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.1
VitrificationCryogen name: ETHANE

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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 / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 µm
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

Startup modelType of model: INSILICO MODEL / Details: AlphaFold II predicted model AF-P16639-F1
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 523915

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