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- EMDB-47566: Cryo-EM structure of Saccharomyces cerevisiae Pmt4-Ccw5 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-47566
TitleCryo-EM structure of Saccharomyces cerevisiae Pmt4-Ccw5 complex
Map datastructure of Saccharomyces cerevisiae Pmt4-Ccw5 complex
Sample
  • Complex: Pmt4-Ccw5 complex
    • Protein or peptide: Dolichyl-phosphate-mannose--protein mannosyltransferase 4
    • Protein or peptide: Cell wall mannoprotein CIS3
  • Ligand: (3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl dihydrogen phosphate
KeywordsPmt4 / O-mannosylation / MEMBRANE PROTEIN
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 / structural constituent of cell wall / fungal-type cell wall biogenesis / protein O-linked glycosylation via mannose / fungal-type cell wall organization / cellular bud tip / fungal-type cell wall ...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 / structural constituent of cell wall / fungal-type cell wall biogenesis / protein O-linked glycosylation via mannose / fungal-type cell wall organization / cellular bud tip / fungal-type cell wall / protein O-linked glycosylation / fungal-type vacuole / cell periphery / endoplasmic reticulum membrane / endoplasmic reticulum / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Yeast PIR protein repeat / : / : / Yeast PIR protein repeat / Cell wall mannoprotein PIR1-like, C-terminal domain / Yeast PIR proteins repeats signature. / Yeast PIR proteins repeats profile. / Glycosyl transferase family 39/83 / Glycosyltransferase 39-like / Protein O-mannosyl-transferase, C-terminal four TM domain ...Yeast PIR protein repeat / : / : / Yeast PIR protein repeat / Cell wall mannoprotein PIR1-like, C-terminal domain / Yeast PIR proteins repeats signature. / Yeast PIR proteins repeats profile. / 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 / Cell wall mannoprotein CIS3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 30, 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_47566.png

Downloads & links

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Map

FileDownload / File: emd_47566.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of Saccharomyces cerevisiae Pmt4-Ccw5 complex
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: 0.023
Minimum - Maximum-0.06279099 - 0.1064989
Average (Standard dev.)0.0010221893 (±0.0053467466)
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_47566_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_47566_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-Ccw5 complex

EntireName: Pmt4-Ccw5 complex
Components
  • Complex: Pmt4-Ccw5 complex
    • Protein or peptide: Dolichyl-phosphate-mannose--protein mannosyltransferase 4
    • Protein or peptide: Cell wall mannoprotein CIS3
  • Ligand: (3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl dihydrogen phosphate

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Supramolecule #1: Pmt4-Ccw5 complex

SupramoleculeName: Pmt4-Ccw5 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: Cell wall mannoprotein CIS3

MacromoleculeName: Cell wall mannoprotein CIS3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.556673 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
TSTNATSSSC ATPSLK

UniProtKB: Cell wall mannoprotein CIS3

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Macromolecule #3: (3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-...

MacromoleculeName: (3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl dihydrogen phosphate
type: ligand / ID: 3 / Number of copies: 1 / Formula: NNM
Molecular weightTheoretical: 644.947 Da
Chemical component information

ChemComp-NNM:
(3R)-3,31-dimethyl-7,11,15,19,23,27-hexamethylidenedotriacont-31-en-1-yl dihydrogen phosphate

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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: OTHER / Details: Pmt4 apo form
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93521
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-9e6i:
Cryo-EM structure of Saccharomyces cerevisiae Pmt4-Ccw5 complex

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