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- EMDB-29338: Cryo-EM structure of Cryptococcus neoformans trehalose-6-phosphat... -

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Basic information

Entry
Database: EMDB / ID: EMD-29338
TitleCryo-EM structure of Cryptococcus neoformans trehalose-6-phosphate synthase homotetramer in apo form
Map dataCryptococcus neoformans trehalose-6-phosphate synthase (Tps1) homotetramer in the apo form
Sample
  • Complex: trehalose-6-phosphate synthase homotetramer in apo form
    • Protein or peptide: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
KeywordsGlycosyltransferase / complex / transferase
Function / homologyGlycosyl transferase, family 20 / Glycosyltransferase family 20 / trehalose biosynthetic process / hexosyltransferase activity / Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
Function and homology information
Biological speciesCryptococcus neoformans var. grubii H99 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWashington EJ / Brennan RG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI104533-01A1 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Cryptococcus neoformans trehalose-6-phosphate synthase homotetramer in apo form
Authors: Washington EJ / Brennan RG
History
DepositionDec 29, 2022-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29338.png

Downloads & links

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Map

FileDownload / File: emd_29338.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryptococcus neoformans trehalose-6-phosphate synthase (Tps1) homotetramer in the apo form
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 320 pix.
= 208. Å		0.65 Å/pix.
x 320 pix.
= 208. Å		0.65 Å/pix.
x 320 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-1.0873547 - 1.8003098
Average (Standard dev.)-0.00048926607 (±0.06881327)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryptococcus neoformans trehalose-6-phosphate synthase (Tps1) homotetramer in the...

Fileemd_29338_half_map_1.map
AnnotationCryptococcus neoformans trehalose-6-phosphate synthase (Tps1) homotetramer in the apo half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryptococcus neoformans trehalose-6-phosphate synthase (Tps1) homotetramer in the...

Fileemd_29338_half_map_2.map
AnnotationCryptococcus neoformans trehalose-6-phosphate synthase (Tps1) homotetramer in the apo half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : trehalose-6-phosphate synthase homotetramer in apo form

EntireName: trehalose-6-phosphate synthase homotetramer in apo form
Components
  • Complex: trehalose-6-phosphate synthase homotetramer in apo form
    • Protein or peptide: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)

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Supramolecule #1: trehalose-6-phosphate synthase homotetramer in apo form

SupramoleculeName: trehalose-6-phosphate synthase homotetramer in apo form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cryptococcus neoformans var. grubii H99 (fungus)
Molecular weightTheoretical: 307 KDa

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Macromolecule #1: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)

MacromoleculeName: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cryptococcus neoformans var. grubii H99 (fungus)
Molecular weightTheoretical: 76.8155 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHSSG VDLGTENLYF QSNAMTTMSN DIPNSPTSTS FTGTFSPAAT AANTAANART SDAPSPTTSS SGPKLETSKE QRLIVVSNR LPVTISKDDN GEYHFKMSSG GLVSALSGCK KTMSFTWIGW PGKDIPMQDR ETVNRRLLDE YNCYPVYLSD E LADSHYNG ...String:
MHHHHHHSSG VDLGTENLYF QSNAMTTMSN DIPNSPTSTS FTGTFSPAAT AANTAANART SDAPSPTTSS SGPKLETSKE QRLIVVSNR LPVTISKDDN GEYHFKMSSG GLVSALSGCK KTMSFTWIGW PGKDIPMQDR ETVNRRLLDE YNCYPVYLSD E LADSHYNG FSNSILWPLF HYHPGEMNFD AAHWLAYREA NMRFADVVSS LVQAGDMVWV QDYHLMLLPM LLRSMITGES AQ GEMVRQE LGRVKEGVDD TVVKEVLKMG PGVAQAEDEG VEMLDDVEEE GGEMDVKSSP KRPHYARGMS TFQKQELVAK EKG KEGIRI GFFLHTPFPS SEIYRILPVR REILLGVLQC DLIGFHTYDY ARHFLSSCTR ILGLETQPNG IEFDGRYCQV GTFP IGIDP NQFIEGLQKE SIVKRLRSLE ARFEGVKVII GVDRLDYIKG IPQKLQALET FLTQHPEWIG KVVLVQLAIP SRQDV EEYQ DLRACVNELV GRINGRFGTV ESVPIHYMHK SVPFEELTAM YALADACLVT STRDGMNLVA YEYISSQAER HGSMIL SEF AGAAQSFNGS LLINPWDVQS TADAINQALT LSPQQRKTNW QKLFNYVSKY TAEAWGVSFV NELNRLSGQR PSGPTGL AG RRKSGSLSRT SSKASIQRRK SSQSGIVTGL GAAAGAAVNW AQAQVQGGSQ T

UniProtKB: Alpha,alpha-trehalose-phosphate synthase (UDP-forming)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207081
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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