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- EMDB-27696: Cryo-EM structure of the full length Arabidopsis SPY with complet... -

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Basic information

Entry
Database: EMDB / ID: EMD-27696
TitleCryo-EM structure of the full length Arabidopsis SPY with complete TPRs
Map data
Sample
  • Complex: Apo SPY
    • Protein or peptide: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
KeywordsO-Fucosyltransferase / SPY / TRANSFERASE
Function / homology
Function and homology information


negative regulation of gibberellic acid mediated signaling pathway / protein N-acetylglucosaminyltransferase activity / protein O-linked fucosylation / peptide-O-fucosyltransferase / gibberellic acid mediated signaling pathway / peptide-O-fucosyltransferase activity / cytokinin-activated signaling pathway / RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity / RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity / protein O-GlcNAc transferase ...negative regulation of gibberellic acid mediated signaling pathway / protein N-acetylglucosaminyltransferase activity / protein O-linked fucosylation / peptide-O-fucosyltransferase / gibberellic acid mediated signaling pathway / peptide-O-fucosyltransferase activity / cytokinin-activated signaling pathway / RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity / RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity / protein O-GlcNAc transferase / flower development / regulation of reactive oxygen species metabolic process / rhythmic process / cell differentiation / nucleus / cytoplasm
Similarity search - Function
: / Sel1-like repeat / Sel1-like repeats. / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. ...: / Sel1-like repeat / Sel1-like repeats. / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKumar S / Zhou Y / Dillard L / Borgnia MJ / Bartesaghi A / Zhou P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structure of the full length Arabidopsis SPY with complete TPRs
Authors: Kumar S / Zhou Y
History
DepositionJul 25, 2022-
Header (metadata) releaseMar 8, 2023-
Map releaseMar 8, 2023-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27696.png

Downloads & links

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Map

FileDownload / File: emd_27696.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 384 pix.
= 337.92 Å		0.88 Å/pix.
x 384 pix.
= 337.92 Å		0.88 Å/pix.
x 384 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-32.946804 - 61.92295
Average (Standard dev.)0.0009202288 (±1.0003834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 337.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27696_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27696_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_27696_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 SPY

EntireName: Apo SPY
Components
  • Complex: Apo SPY
    • Protein or peptide: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY

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Supramolecule #1: Apo SPY

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

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Macromolecule #1: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltra...

MacromoleculeName: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein O-GlcNAc transferase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 105.278859 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVGLEDDTER ERSPVVENGF SNGSRSSSSS AGVLSPSRKV TQGNDTLSYA NILRARNKFA DALALYEAML EKDSKNVEAH IGKGICLQT QNKGNLAFDC FSEAIRLDPH NACALTHCGI LHKEEGRLVE AAESYQKALM ADASYKPAAE CLAIVLTDLG T SLKLAGNT ...String:
MVGLEDDTER ERSPVVENGF SNGSRSSSSS AGVLSPSRKV TQGNDTLSYA NILRARNKFA DALALYEAML EKDSKNVEAH IGKGICLQT QNKGNLAFDC FSEAIRLDPH NACALTHCGI LHKEEGRLVE AAESYQKALM ADASYKPAAE CLAIVLTDLG T SLKLAGNT QEGIQKYYEA LKIDPHYAPA YYNLGVVYSE MMQYDNALSC YEKAALERPM YAEAYCNMGV IYKNRGDLEM AI TCYERCL AVSPNFEIAK NNMAIALTDL GTKVKLEGDV TQGVAYYKKA LYYNWHYADA MYNLGVAYGE MLKFDMAIVF YEL AFHFNP HCAEACNNLG VLYKDRDNLD KAVECYQMAL SIKPNFAQSL NNLGVVYTVQ GKMDAAASMI EKAILANPTY AEAF NNLGV LYRDAGNITM AIDAYEECLK IDPDSRNAGQ NRLLAMNYIN EGLDDKLFEA HRDWGWRFTR LHPQYTSWDN LKDPE RPIT IGYISPDFFT HSVSYFIEAP LTHHDYTKYK VVVYSAVVKA DAKTYRFRDK VLKKGGVWKD IYGIDEKKIA SMVRED KID ILVELTGHTA NNKLGTMACR PAPVQVTWIG YPNTTGLPTV DYRITDSLAD PPDTKQKQVE ELVRLPDCFL CYTPSPE AG PVCPTPALSN GFVTFGSFNN LAKITPKVLQ VWARILCAVP NSRLVVKCKP FCCDSIRQRF LTTLEQLGLE SKRVDLLP L ILFNHDHMQA YSLMDISLDT FPYAGTTTTC ESLYMGVPCV TMAGSVHAHN VGVSLLTKVG LGHLVAKNED EYVQLSVDL ASDVTALSKL RMSLRDLMAG SPVCNGPSFA VGLESAYRNM WKKYCKGEVP SLRRMEMLQK EVHDDPLISK DLGPSRVSVT GEATPSLKA NGSAPVPSSL PTQSPQLSKR MDSTSGGSEN LYFQGGSHHH HHHHHHHGGW SHPQFEK

UniProtKB: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY

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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

Concentration0.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloride
2.0 mMC4H10O2S21,4-dithiothreitol
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 289.15 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 54900
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 91837
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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