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- EMDB-27699: Cryo-EM structure of Arabidopsis SPY in complex with GDP-fucose -

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Basic information

Entry
Database: EMDB / ID: EMD-27699
TitleCryo-EM structure of Arabidopsis SPY in complex with GDP-fucose
Map data
Sample
  • Complex: SPY in complex with GDP-fucose
    • Protein or peptide: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
  • Ligand: GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE
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: 3.8 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_27699.png

Downloads & links

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Map

FileDownload / File: emd_27699.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.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.4
Minimum - Maximum-41.943108000000002 - 56.301192999999998
Average (Standard dev.)0.0019954871 (±0.9764749)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Overall lower resolution map

Fileemd_27699_additional_1.map
AnnotationOverall lower resolution map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused component map (monomer B)

Fileemd_27699_additional_2.map
AnnotationFocused component map (monomer B)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused component map (monomer A)

Fileemd_27699_additional_3.map
AnnotationFocused component map (monomer A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SPY in complex with GDP-fucose

EntireName: SPY in complex with GDP-fucose
Components
  • Complex: SPY in complex with GDP-fucose
    • Protein or peptide: Probable UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase SPINDLY
  • Ligand: GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE

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Supramolecule #1: SPY in complex with GDP-fucose

SupramoleculeName: SPY in complex with GDP-fucose / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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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Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE / type: ligand / ID: 2 / Number of copies: 2 / Formula: GFB
Molecular weightTheoretical: 589.342 Da
Chemical component information

ChemComp-GFB:
GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE

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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
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.4 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 182947
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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