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- EMDB-37612: Structure of 1,3-beta-glucan synthase component FKS1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-37612
TitleStructure of 1,3-beta-glucan synthase component FKS1
Map data
Sample
  • Complex: 1,3-beta-glucan synthase component FKS1 in apo state
    • Protein or peptide: 1,3-beta-glucan synthase component FKS1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


fungal-type cell wall polysaccharide biosynthetic process / 1,3-beta-glucan synthase / 1,3-beta-D-glucan synthase activity / (1->3)-beta-D-glucan biosynthetic process / 1,3-beta-D-glucan synthase complex / fungal-type cell wall biogenesis / cellular bud / ascospore wall assembly / cellular bud tip / actin cortical patch ...fungal-type cell wall polysaccharide biosynthetic process / 1,3-beta-glucan synthase / 1,3-beta-D-glucan synthase activity / (1->3)-beta-D-glucan biosynthetic process / 1,3-beta-D-glucan synthase complex / fungal-type cell wall biogenesis / cellular bud / ascospore wall assembly / cellular bud tip / actin cortical patch / fungal-type cell wall / cellular bud neck / regulation of cell size / positive regulation of endocytosis / cell periphery / mitochondrion / plasma membrane
Similarity search - Function
Glycosyl transferase, family 48 / 1,3-beta-glucan synthase subunit FKS1-like, domain-1 / 1,3-beta-glucan synthase component / 1,3-beta-glucan synthase subunit FKS1, domain-1 / 1,3-beta-glucan synthase subunit FKS1
Similarity search - Domain/homology
1,3-beta-glucan synthase component FKS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsLi JL / Zhu AQ / Liu JX / Dai XL / Wang X / Yan CY / Deng D
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of 1,3-beta-glucan synthase component FKS1
Authors: Li JL / Zhu AQ / Liu JX / Dai XL / Wang X / Yan CY / Deng D
History
DepositionSep 29, 2023-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37612.png

Downloads & links

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Map

FileDownload / File: emd_37612.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.178
Minimum - Maximum-1.7297057 - 2.7981076
Average (Standard dev.)0.0015650587 (±0.047973026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37612_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37612_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_37612_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 : 1,3-beta-glucan synthase component FKS1 in apo state

EntireName: 1,3-beta-glucan synthase component FKS1 in apo state
Components
  • Complex: 1,3-beta-glucan synthase component FKS1 in apo state
    • Protein or peptide: 1,3-beta-glucan synthase component FKS1

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Supramolecule #1: 1,3-beta-glucan synthase component FKS1 in apo state

SupramoleculeName: 1,3-beta-glucan synthase component FKS1 in apo state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: 1,3-beta-glucan synthase component FKS1

MacromoleculeName: 1,3-beta-glucan synthase component FKS1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: 1,3-beta-glucan synthase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 215.076156 KDa
SequenceString: MNTDQQPYQG QTDYTQGPGN GQSQEQDYDQ YGQPLYPSQA DGYYDPNVAA GTEADMYGQQ PPNESYDQDY TNGEYYGQPP NMAAQDGEN FSDFSSYGPP GTPGYDSYGG QYTASQMSYG EPNSSGTSTP IYGNYDPNAI AMALPNEPYP AWTADSQSPV S IEQIEDIF ...String:
MNTDQQPYQG QTDYTQGPGN GQSQEQDYDQ YGQPLYPSQA DGYYDPNVAA GTEADMYGQQ PPNESYDQDY TNGEYYGQPP NMAAQDGEN FSDFSSYGPP GTPGYDSYGG QYTASQMSYG EPNSSGTSTP IYGNYDPNAI AMALPNEPYP AWTADSQSPV S IEQIEDIF IDLTNRLGFQ RDSMRNMFDH FMVLLDSRSS RMSPDQALLS LHADYIGGDT ANYKKWYFAA QLDMDDEIGF RN MSLGKLS RKARKAKKKN KKAMEEANPE DTEETLNKIE GDNSLEAADF RWKAKMNQLS PLERVRHIAL YLLCWGEANQ VRF TAECLC FIYKCALDYL DSPLCQQRQE PMPEGDFLNR VITPIYHFIR NQVYEIVDGR FVKRERDHNK IVGYDDLNQL FWYP EGIAK IVLEDGTKLI ELPLEERYLR LGDVVWDDVF FKTYKETRTW LHLVTNFNRI WVMHISIFWM YFAYNSPTFY THNYQ QLVD NQPLAAYKWA SCALGGTVAS LIQIVATLCE WSFVPRKWAG AQHLSRRFWF LCIIFGINLG PIIFVFAYDK DTVYST AAH VVAAVMFFVA VATIIFFSIM PLGGLFTSYM KKSTRRYVAS QTFTAAFAPL HGLDRWMSYL VWVTVFAAKY SESYYFL VL SLRDPIRILS TTAMRCTGEY WWGAVLCKVQ PKIVLGLVIA TDFILFFLDT YLWYIIVNTI FSVGKSFYLG ISILTPWR N IFTRLPKRIY SKILATTDME IKYKPKVLIS QVWNAIIISM YREHLLAIDH VQKLLYHQVP SEIEGKRTLR APTFFVSQD DNNFETEFFP RDSEAERRIS FFAQSLSTPI PEPLPVDNMP TFTVLTPHYA ERILLSLREI IREDDQFSRV TLLEYLKQLH PVEWECFVK DTKILAEETA AYEGNENEAE KEDALKSQID DLPFYCIGFK SAAPEYTLRT RIWASLRSQT LYRTISGFMN Y SRAIKLLY RVENPEIVQM FGGNAEGLER ELEKMARRKF KFLVSMQRLA KFKPHELENA EFLLRAYPDL QIAYLDEEPP LT EGEEPRI YSALIDGHCE ILDNGRRRPK FRVQLSGNPI LGDGKSDNQN HALIFYRGEY IQLIDANQDN YLEECLKIRS VLA EFEELN VEQVNPYAPG LRYEEQTTNH PVAIVGAREY IFSENSGVLG DVAAGKEQTF GTLFARTLSQ IGGKLHYGHP DFIN ATFMT TRGGVSKAQK GLHLNEDIYA GMNAMLRGGR IKHCEYYQCG KGRDLGFGTI LNFTTKIGAG MGEQMLSREY YYLGT QLPV DRFLTFYYAH PGFHLNNLFI QLSLQMFMLT LVNLSSLAHE SIMCIYDRNK PKTDVLVPIG CYNFQPAVDW VRRYTL SIF IVFWIAFVPI VVQELIERGL WKATQRFFCH LLSLSPMFEV FAGQIYSSAL LSDLAIGGAR YISTGRGFAT SRIPFSI LY SRFAGSAIYM GARSMLMLLF GTVAHWQAPL LWFWASLSSL IFAPFVFNPH QFAWEDFFLD YRDYIRWLSR GNNQYHRN S WIGYVRMSRA RITGFKRKLV GDESEKAAGD ASRAHRTNLI MAEIIPCAIY AAGCFIAFTF INAQTGVKTT DDDRVNSVL RIIICTLAPI AVNLGVLFFC MGMSCCSGPL FGMCCKKTGS VMAGIAHGVA VIVHIAFFIV MWVLESFNFV RMLIGVVTCI QCQRLIFHC MTALMLTREF KNDHANTAFW TGKWYGKGMG YMAWTQPSRE LTAKVIELSE FAADFVLGHV ILICQLPLII I PKIDKFHS IMLFWLKPSR QIRPPIYSLK QTRLRKRMVK KYCSLYFLVL AIFAGCIIGP AVASAKIHKH IGDSLDGVVH NL FQPINTT NNDTGSQMST YQSHYYTHTP SLKTWSTIK

UniProtKB: 1,3-beta-glucan synthase component FKS1

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 53.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.1 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: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 277867
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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