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- EMDB-66154: The cryo-EM structural analysis of full-length PyrN -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-66154
TitleThe cryo-EM structural analysis of full-length PyrN
Map data
Sample
  • Complex: Methionine-tRNA ligase homo-dimer
    • Protein or peptide: Methionine-tRNA ligase
KeywordspyrN / Aminoacyl-tRNA synthetase / LIGASE
Biological speciesStreptomyces candidus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsFeng Y / Du YL
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The cryo-EM structural analysis of full-length PyrN
Authors: Feng Y / Du YL
History
DepositionSep 10, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66154.png

Downloads & links

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Map

FileDownload / File: emd_66154.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 200 pix.
= 240. Å		1.2 Å/pix.
x 200 pix.
= 240. Å		1.2 Å/pix.
x 200 pix.
= 240. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.239
Minimum - Maximum-1.6027311 - 2.238802
Average (Standard dev.)-0.0010459203 (±0.05129471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 240.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66154_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_66154_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 : Methionine-tRNA ligase homo-dimer

EntireName: Methionine-tRNA ligase homo-dimer
Components
  • Complex: Methionine-tRNA ligase homo-dimer
    • Protein or peptide: Methionine-tRNA ligase

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Supramolecule #1: Methionine-tRNA ligase homo-dimer

SupramoleculeName: Methionine-tRNA ligase homo-dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptomyces candidus (bacteria)

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Macromolecule #1: Methionine-tRNA ligase

MacromoleculeName: Methionine-tRNA ligase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptomyces candidus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIVSEIPREL ADLARADFVR SAAPAWAEAA GVPFNVRRVT LRPGETTAEH NHHDLEVWVM LDGVGEVGWD GHQRVLTAGD SVYLPPLAPH TLRNLSSDRP LSFFSMWWEN LSALAAVHAE RREQAVERQG RPVLLLPSFP TPNGELHLGH LSGPFLNADA CRRALLAAGE ...String:
MIVSEIPREL ADLARADFVR SAAPAWAEAA GVPFNVRRVT LRPGETTAEH NHHDLEVWVM LDGVGEVGWD GHQRVLTAGD SVYLPPLAPH TLRNLSSDRP LSFFSMWWEN LSALAAVHAE RREQAVERQG RPVLLLPSFP TPNGELHLGH LSGPFLNADA CRRALLAAGE RAHLLLGTVG HQSQVSAAAE AEGLSFHELA ERNTDAIIEG LQAAGIDWDV FVRPSEPAYP AMATSVFESL RDRGVLVRRT EPTNYCEPCG RFLLEAFVAG HCPHCGSNQT AGIECELCAL PYDDRDLVDP SCATCGAAAT QRPLTRYFMP LEPLRDELSG YLRGAAMHGR LRAYTERVLA KTLPDLPVSI PAEHGIPIHV EDASGPAEQR MYSAFELAAR FLTALDGFAD GWEAYARQEN PRTVLFFGFD NAFLRAFAFP AVLGAFTDAL PLPEALVCND FYLLDGEKFS TGRKHAVWAR QAVTPANADQ LRLYLAATSP DVRRRDFTTR GYAEFVTAEL IGRWQRRLDD VGGRVAEHFG GLTPEAGGWH AEAERFYGQI KEFASCATLD YLPGRFKPRA VVAAACAFIR QAEDFAEVSA DATPGSGIAR TCAALELMAL RTLAMAVWPL APEFGRRVAA ALGEDTIALE PTPRWVRPDT EIKFATDHFS PDEVVAGR

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 345810
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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