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- EMDB-47541: Cryo-EM structure of Saccharomyces cerevisiae Pmt4 apo form -

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Basic information

Entry
Database: EMDB / ID: EMD-47541
TitleCryo-EM structure of Saccharomyces cerevisiae Pmt4 apo form
Map datastructure of Saccharomyces cerevisiae Pmt4 apo form
Sample
  • Complex: Pmt4 homo dimer
    • Protein or peptide: Dolichyl-phosphate-mannose--protein mannosyltransferase 4
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
KeywordsPmt4 / O-mannosylation / TRANSFERASE
Function / homology
Function and homology information


dolichyl-phosphate-mannose-protein mannosyltransferase Pmt4p homodimer complex / dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / regulation of endoplasmic reticulum unfolded protein response / fungal-type cell wall biogenesis / protein O-linked glycosylation via mannose / protein O-linked glycosylation / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding
Similarity search - Function
Glycosyl transferase family 39/83 / Glycosyltransferase 39-like / Protein O-mannosyl-transferase, C-terminal four TM domain / Dolichyl-phosphate-mannose-protein mannosyltransferase / C-terminal four TMM region of protein-O-mannosyltransferase / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily
Similarity search - Domain/homology
Dolichyl-phosphate-mannose--protein mannosyltransferase 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsDu M / Yuan Z / Li H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA231466 United States
Department of Energy (DOE, United States)GM131754 United States
CitationJournal: To Be Published
Title: Pmt4 recognizes two separate acceptor sites to O-mannosylate the S/T-rich regions of substrate proteins
Authors: Du M / Yuan Z / Li H
History
DepositionOct 29, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47541.png

Downloads & links

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Map

FileDownload / File: emd_47541.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of Saccharomyces cerevisiae Pmt4 apo form
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 200 pix.
= 165.6 Å		0.83 Å/pix.
x 200 pix.
= 165.6 Å		0.83 Å/pix.
x 200 pix.
= 165.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.06283729 - 0.09510951
Average (Standard dev.)0.0010020492 (±0.004875331)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 165.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_47541_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_47541_half_map_2.map
AnnotationHalf Map 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 : Pmt4 homo dimer

EntireName: Pmt4 homo dimer
Components
  • Complex: Pmt4 homo dimer
    • Protein or peptide: Dolichyl-phosphate-mannose--protein mannosyltransferase 4
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

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Supramolecule #1: Pmt4 homo dimer

SupramoleculeName: Pmt4 homo dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Dolichyl-phosphate-mannose--protein mannosyltransferase 4

MacromoleculeName: Dolichyl-phosphate-mannose--protein mannosyltransferase 4
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: dolichyl-phosphate-mannose-protein mannosyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 88.061945 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSVPKKRNHG KLPPSTKDVD DPSLKYTKAA PKCEQVAEHW LLQPLPEPES RYSFWVTIVT LLAFAARFYK IWYPKEVVFD EVHFGKFAS YYLERSYFFD VHPPFAKMMI AFIGWLCGYD GSFKFDEIGY SYETHPAPYI AYRSFNAILG TLTVPIMFNT L KELNFRAI ...String:
MSVPKKRNHG KLPPSTKDVD DPSLKYTKAA PKCEQVAEHW LLQPLPEPES RYSFWVTIVT LLAFAARFYK IWYPKEVVFD EVHFGKFAS YYLERSYFFD VHPPFAKMMI AFIGWLCGYD GSFKFDEIGY SYETHPAPYI AYRSFNAILG TLTVPIMFNT L KELNFRAI TCAFASLLVA IDTAHVTETR LILLDAILII SIAATMYCYV RFYKCQLRQP FTWSWYIWLH ATGLSLSFVI ST KYVGVMT YSAIGFAAVV NLWQLLDIKA GLSLRQFMRH FSKRLNGLVL IPFVIYLFWF WVHFTVLNTS GPGDAFMSAE FQE TLKDSP LSVDSKTVNY FDIITIKHQD TDAFLHSHLA RYPQRYEDGR ISSAGQQVTG YTHPDFNNQW EVLPPHGSDV GKGQ AVLLN QHIRLRHVAT DTYLLAHDVA SPFYPTNEEI TTVTLEEGDG ELYPETLFAF QPLKKSDEGH VLKSKTVSFR LFHVD TSVA LWTHNDELLP DWGFQQQEIN GNKKVIDPSN NWVVDEIVNL DEVRKVYIPK VVKPLPFLKK WIETQKSMFE HNNKLS SEH PFASEPYSWP GSLSGVSFWT NGDEKKQIYF IGNIIGWWFQ VISLAVFVGI IVADLITRHR GYYALNKMTR EKLYGPL MF FFVSWCCHYF PFFLMARQKF LHHYLPAHLI ACLFSGALWE VIFSDCKSLD LEKDEDISGA SYERNPKVYV KPYTVFLV C VSCAVAWFFV YFSPLVYGDV SLSPSEVVSR EWFDIELNFS K

UniProtKB: Dolichyl-phosphate-mannose--protein mannosyltransferase 4

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Macromolecule #2: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k 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: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92548
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9e61:
Cryo-EM structure of Saccharomyces cerevisiae Pmt4 apo form

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