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

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Basic information

Entry
Database: PDB / ID: 9.0E+61
TitleCryo-EM structure of Saccharomyces cerevisiae Pmt4 apo form
ComponentsDolichyl-phosphate-mannose--protein mannosyltransferase 4
KeywordsTRANSFERASE / Pmt4 / O-mannosylation
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
Chem-CPL / Dolichyl-phosphate-mannose--protein mannosyltransferase 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsDu, M. / Yuan, Z. / Li, H.
Funding support United States, 2items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 15, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dolichyl-phosphate-mannose--protein mannosyltransferase 4
B: Dolichyl-phosphate-mannose--protein mannosyltransferase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,6404
Polymers176,1242
Non-polymers1,5162
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 88061.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PMT4, YJR143C, J2176 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P46971, dolichyl-phosphate-mannose-protein mannosyltransferase
#2: Chemical ChemComp-CPL / 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITOYL-LINOLEOYL PHOSPHATIDYLCHOLINE


Mass: 758.060 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H80NO8P / Comment: phospholipid*YM
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pmt4 homo dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92548 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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