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- EMDB-65054: Cryo-EM structure of AtNUTECD in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-65054
TitleCryo-EM structure of AtNUTECD in apo state
Map data
Sample
  • Complex: AtNUTECD
    • Protein or peptide: AT5G25930 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAtNUTECD / Apo / HORMONE
Function / homology
Function and homology information


protein kinase activity / ATP binding / membrane
Similarity search - Function
: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat ...: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsXu Y / Wei X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of AtNUTECD
Authors: Xu Y / Wei X
History
DepositionJun 16, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65054.png

Downloads & links

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Map

FileDownload / File: emd_65054.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.58 Å/pix.
x 320 pix.
= 184. Å		0.58 Å/pix.
x 320 pix.
= 184. Å		0.58 Å/pix.
x 320 pix.
= 184. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.575 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.59584177 - 0.8784345
Average (Standard dev.)0.00007100496 (±0.02217729)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 184.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65054_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_65054_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 : AtNUTECD

EntireName: AtNUTECD
Components
  • Complex: AtNUTECD
    • Protein or peptide: AT5G25930 protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: AtNUTECD

SupramoleculeName: AtNUTECD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: AT5G25930 protein

MacromoleculeName: AT5G25930 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 93.232539 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTRLPLPFLF FFLTSIPLSV FSQFNDQSTL LNLKRDLGDP PSLRLWNNTS SPCNWSEITC TAGNVTGINF KNQNFTGTVP TTICDLSNL NFLDLSFNYF AGEFPTVLYN CTKLQYLDLS QNLLNGSLPV DIDRLSPELD YLDLAANGFS GDIPKSLGRI S KLKVLNLY ...String:
MTRLPLPFLF FFLTSIPLSV FSQFNDQSTL LNLKRDLGDP PSLRLWNNTS SPCNWSEITC TAGNVTGINF KNQNFTGTVP TTICDLSNL NFLDLSFNYF AGEFPTVLYN CTKLQYLDLS QNLLNGSLPV DIDRLSPELD YLDLAANGFS GDIPKSLGRI S KLKVLNLY QSEYDGTFPS EIGDLSELEE LRLALNDKFT PAKIPIEFGK LKKLKYMWLE EMNLIGEISP VVFENMTDLE HV DLSVNNL TGRIPDVLFG LKNLTEFYLF ANGLTGEIPK SISATNLVFL DLSANNLTGS IPVSIGNLTK LQVLNLFNNK LTG EIPPVI GKLPGLKEFK IFNNKLTGEI PAEIGVHSKL ERFEVSENQL TGKLPENLCK GGKLQGVVVY SNNLTGEIPE SLGD CGTLL TVQLQNNDFS GKFPSRIWNA SSMYSLQVSN NSFTGELPEN VAWNMSRIEI DNNRFSGEIP KKIGTWSSLV EFKAG NNQF SGEFPKELTS LSNLISIFLD ENDLTGELPD EIISWKSLIT LSLSKNKLSG EIPRALGLLP RLLNLDLSEN QFSGGI PPE IGSLKLTTFN VSSNRLTGGI PEQLDNLAYE RSFLNNSNLC ADNPVLSLPD CRKQRRGSRG FPGKILAMIL VIAVLLL TI TLFVTFFVVR DYTRKQRRRG LETWKLTSFH RVDFAESDIV SNLMKHYVIG SGGSGKVYKI FVESSGQCVA VKRIWDSK K LDQKLEKEFI AEVEILGTIR HSNIVKLLCC ISREDSKLLV YEYLEKRSLD QWLHGKKKGG TVEANNLTWS QRLNIAVGA AQGLCYMHHD CTPAIIHRDV KSSNILLDSE FNAKI

UniProtKB: AT5G25930 protein

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 6
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: 1.6 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 215000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: AlphaFold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 386629
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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