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- PDB-9e79: Crystal structure of the MIR domain of the S. cerevisiae mannosyl... -

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Basic information

Entry
Database: PDB / ID: 9.0E+79
TitleCrystal structure of the MIR domain of the S. cerevisiae mannosyltransferase Pmt4
ComponentsDolichyl-phosphate-mannose--protein mannosyltransferase 4
KeywordsMEMBRANE PROTEIN / Saccharomyces cerevisiae / 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
Dolichyl-phosphate-mannose--protein mannosyltransferase 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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
DepositionNov 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: 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
C: Dolichyl-phosphate-mannose--protein mannosyltransferase 4


Theoretical massNumber of molelcules
Total (without water)66,7943
Polymers66,7943
Non-polymers00
Water10,971609
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.091, 54.942, 118.661
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-224-

HOH

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Components

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


Mass: 22264.555 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PMT4, YJR143C, J2176 / Production host: Escherichia coli (E. coli)
References: UniProt: P46971, dolichyl-phosphate-mannose-protein mannosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0 M LiCl, 0.1 M citric acid, and 30% PEG 6000 (w/v) at pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97931 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.64→47.58 Å / Num. obs: 163344 / % possible obs: 97.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.48
Reflection shellResolution: 1.64→1.67 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 1.32 / Num. unique obs: 2222

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Processing

Software
NameVersionClassification
PHENIX1.21.2-5419refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→14.83 Å / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 26.7 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.22 2102 2.88 %
Rwork0.1992 --
obs0.2116 73086 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→14.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4679 0 0 609 5288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064831
X-RAY DIFFRACTIONf_angle_d0.8676595
X-RAY DIFFRACTIONf_dihedral_angle_d16.0891722
X-RAY DIFFRACTIONf_chiral_restr0.056720
X-RAY DIFFRACTIONf_plane_restr0.007867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.33721460.30815099X-RAY DIFFRACTION96
1.68-1.730.35031440.31365152X-RAY DIFFRACTION96
1.73-1.780.3561360.29925035X-RAY DIFFRACTION95
1.78-1.830.30611540.28965081X-RAY DIFFRACTION94
1.83-1.90.28181290.27774724X-RAY DIFFRACTION89
1.9-1.980.24941390.26465073X-RAY DIFFRACTION95
1.98-2.070.26681450.24735114X-RAY DIFFRACTION96
2.07-2.170.28981390.23545215X-RAY DIFFRACTION97
2.17-2.310.28731410.22075105X-RAY DIFFRACTION96
2.31-2.490.29131490.21055057X-RAY DIFFRACTION95
2.49-2.740.27521330.20224812X-RAY DIFFRACTION89
2.74-3.130.22931320.18035183X-RAY DIFFRACTION97
3.13-3.930.18131520.14765231X-RAY DIFFRACTION96
3.93-14.830.19161370.14875229X-RAY DIFFRACTION95

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