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- PDB-9fd1: Structure of the Chaetomium thermophilum Pmt4-MIR domain with bou... -

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Basic information

Entry
Database: PDB / ID: 9fd1
TitleStructure of the Chaetomium thermophilum Pmt4-MIR domain with bound ligands
ComponentsDolichyl-phosphate-mannose--protein mannosyltransferase
KeywordsPEPTIDE BINDING PROTEIN / Protein O-mannosylation / glycosylation / ER luminal domain / b-trefoil / thermostability / ligand binding / processivity
Function / homology
Function and homology information


dolichyl-phosphate-mannose-protein mannosyltransferase / dolichyl-phosphate-mannose-protein mannosyltransferase activity / endoplasmic reticulum membrane
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
ACETATE ION / Dolichyl-phosphate-mannose--protein mannosyltransferase
Similarity search - Component
Biological speciesChaetomium (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsMcDowell, M.A. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structural characterisation of the fungal Pmt4 homodimer.
Authors: Melanie A McDowell / Klemens Wild / Francesco Fiorentino / Daniela Bausewein / Anke Metschies / Antonella Chiapparino / Yvonne Hackmann / Florestan L Bilsing / David Brenske / Sofia ...Authors: Melanie A McDowell / Klemens Wild / Francesco Fiorentino / Daniela Bausewein / Anke Metschies / Antonella Chiapparino / Yvonne Hackmann / Florestan L Bilsing / David Brenske / Sofia Mortensen / Di Wu / Carol V Robinson / Sabine Strahl / Irmgard Sinning /
Abstract: Protein O-mannosyltransferases (PMTs) are conserved endoplasmic reticulum membrane-embedded enzymes responsible for the transfer of mannose from dolichol phosphate-mannose (Dol-P-Man) to ...Protein O-mannosyltransferases (PMTs) are conserved endoplasmic reticulum membrane-embedded enzymes responsible for the transfer of mannose from dolichol phosphate-mannose (Dol-P-Man) to serine/threonine-rich protein substrates or unfolded proteins. PMTs from three subfamilies form obligate dimers with different substrate specificities and require the concerted action of their transmembrane domains (TMDs) and a luminal MIR domain for catalysis. Here, we present structures, native mass spectrometry, and structure-based mutagenesis of the fungal Pmt4 homodimer. The core fold of the TMDs and MIR domain is conserved with the Pmt1-Pmt2 heterodimer, indicating a shared catalytic mechanism. Distinct from Pmt4, the MIR domain interacts in cis with the TMDs of the same subunit and has a β-hairpin insertion required for O-mannosylation of substrates. We further identify a cytosolic binding site for substrate Dol-P-Man within the Pmt4 TMDs, which is conserved amongst PMTs and important for in vivo activity. Thus, we provide a framework to understand the substrate specificity and regulation of the Pmt4 homodimer.
History
DepositionMay 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,69519
Polymers24,6311
Non-polymers1,06318
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint15 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.155, 100.628, 103.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-618-

NA

21A-829-

HOH

31A-1004-

HOH

41A-1020-

HOH

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Components

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


Mass: 24631.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium (fungus) / Gene: CTHT_0059600 / Production host: Escherichia coli (E. coli)
References: UniProt: G0SET1, dolichyl-phosphate-mannose-protein mannosyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.4 M sodium acetate pH 7, 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.22→36.03 Å / Num. obs: 64952 / % possible obs: 68.62 % / Redundancy: 2 % / CC1/2: 0.995 / Net I/σ(I): 22.83
Reflection shellResolution: 1.22→1.264 Å / Num. unique obs: 497 / CC1/2: 0.685

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→36.03 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1398 2003 3.08 %
Rwork0.1114 --
obs0.1123 64950 67.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 69 373 2119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071831
X-RAY DIFFRACTIONf_angle_d1.1392473
X-RAY DIFFRACTIONf_dihedral_angle_d14.467675
X-RAY DIFFRACTIONf_chiral_restr0.093249
X-RAY DIFFRACTIONf_plane_restr0.011327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.250.364780.2882240X-RAY DIFFRACTION4
1.25-1.280.2443160.2454526X-RAY DIFFRACTION8
1.28-1.320.3116320.2101939X-RAY DIFFRACTION14
1.32-1.360.2756480.19241662X-RAY DIFFRACTION25
1.36-1.410.2534910.18752789X-RAY DIFFRACTION43
1.41-1.470.20311330.15964480X-RAY DIFFRACTION68
1.47-1.530.18361960.14135675X-RAY DIFFRACTION86
1.53-1.610.17082020.12466536X-RAY DIFFRACTION100
1.61-1.710.14142140.11376608X-RAY DIFFRACTION100
1.71-1.850.12482050.10186620X-RAY DIFFRACTION100
1.85-2.030.14452180.09556633X-RAY DIFFRACTION100
2.03-2.330.12762100.09226633X-RAY DIFFRACTION100
2.33-2.930.12812110.10386698X-RAY DIFFRACTION100
2.93-36.030.12592190.11376908X-RAY DIFFRACTION100

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