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- PDB-9e7a: Crystal structure of the MIR domain of the S. cerevisiae mannosyl... -

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Basic information

Entry
Database: PDB / ID: 9e7a
TitleCrystal structure of the MIR domain of the S. cerevisiae mannosyltransferase Pmt4 in Complex with Ccw5
Components
  • Cell wall mannoprotein CIS3
  • Dolichyl-phosphate-mannose--protein mannosyltransferase 4
KeywordsMEMBRANE PROTEIN / Pmt4 / Ccw5 / 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 / 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
DI(HYDROXYETHYL)ETHER / Dolichyl-phosphate-mannose--protein mannosyltransferase 4 / Cell wall mannoprotein CIS3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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

Downloads & links

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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
D: Cell wall mannoprotein CIS3
E: Cell wall mannoprotein CIS3
F: Cell wall mannoprotein CIS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0598
Polymers77,8616
Non-polymers1982
Water7,728429
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.599, 78.850, 118.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 6 through 35 or (resid 36...
d_2ens_1(chain "B" and (resid 6 through 34 or (resid 35...
d_3ens_1(chain "C" and (resid 6 through 34 or (resid 35...
d_1ens_2chain "D"
d_2ens_2chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERGLYGLYAA6 - 686 - 68
d_12ens_1ASPASPGLYGLYAA70 - 7270 - 72
d_13ens_1GLYGLYVALVALAA74 - 19774 - 197
d_21ens_1SERSERGLYGLYBB6 - 686 - 68
d_22ens_1ASPASPGLYGLYBB70 - 7270 - 72
d_23ens_1GLYGLYVALVALBB74 - 19774 - 197
d_31ens_1SERSERGLYGLYCC6 - 686 - 68
d_32ens_1ASPASPGLYGLYCC70 - 7270 - 72
d_33ens_1GLYGLYVALVALCC74 - 19774 - 197
d_11ens_2LYSLYSASNASNDD1 - 56 - 10
d_21ens_2LYSLYSASNASNFF1 - 56 - 10

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.0462357915058, 0.307972031031, -0.950271266369), (0.107026834715, 0.947340057931, 0.301814630678), (0.993180501336, -0.0877498874222, -0.0767622890655)25.3209475561, 12.0447291721, 15.7344997013
2given(-0.503221824622, 0.862905353144, 0.0464988896487), (-0.19989060753, -0.168582049318, 0.96520662952), (0.840720845611, 0.476418349943, 0.257320841737)-7.46149402589, 8.15588616483, 40.9375035334
3given(-0.483490002491, 0.874853308838, 0.0294805954311), (-0.228540264242, -0.158670654367, 0.960517033198), (0.844989210056, 0.457662879704, 0.27665488145)-7.45513713287, 8.31309563296, 40.97139842

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Components

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


Mass: 24090.770 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: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P46971, dolichyl-phosphate-mannose-protein mannosyltransferase
#2: Protein/peptide Cell wall mannoprotein CIS3 / Covalently-linked cell wall protein 5/11 / Protein with internal repeats 4 / Soluble cell wall protein 8


Mass: 1862.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47001
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25% polyethylene glycol monomethyl ether 2000 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: 1.078 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: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.69→51.75 Å / Num. obs: 94643 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.21 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 11.54
Reflection shellResolution: 1.69→1.71 Å / Rmerge(I) obs: 0.198 / Num. unique obs: 4755

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
MOSFLMdata reduction
SCALAdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→51.75 Å / SU ML: 0.2451 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 23.2138
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2266 3628 5.03 %
Rwork0.1895 68487 -
obs0.1913 72115 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.93 Å2
Refinement stepCycle: LAST / Resolution: 1.69→51.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4707 0 13 429 5149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01054846
X-RAY DIFFRACTIONf_angle_d1.13046611
X-RAY DIFFRACTIONf_chiral_restr0.0694734
X-RAY DIFFRACTIONf_plane_restr0.0094859
X-RAY DIFFRACTIONf_dihedral_angle_d16.10611704
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.642695015967
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.626856850422
ens_2d_2DDX-RAY DIFFRACTIONTorsion NCS0.727968941194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.710.39421480.3782536X-RAY DIFFRACTION96.65
1.71-1.740.38181420.36042543X-RAY DIFFRACTION97.89
1.74-1.760.36391590.34582557X-RAY DIFFRACTION98.3
1.76-1.790.36541370.33222545X-RAY DIFFRACTION98.6
1.79-1.810.34631260.32082613X-RAY DIFFRACTION99.17
1.81-1.840.3391120.30362629X-RAY DIFFRACTION99.42
1.84-1.880.29271410.28682619X-RAY DIFFRACTION99.75
1.88-1.910.25951340.26652623X-RAY DIFFRACTION99.71
1.91-1.950.29781440.25682602X-RAY DIFFRACTION99.82
1.95-1.990.28411160.23842632X-RAY DIFFRACTION99.75
1.99-2.030.27511410.23072626X-RAY DIFFRACTION99.53
2.03-2.080.25571500.23452590X-RAY DIFFRACTION98.14
2.08-2.130.25961600.20832594X-RAY DIFFRACTION99.82
2.13-2.190.24321330.18872632X-RAY DIFFRACTION99.96
2.19-2.250.23361270.18462644X-RAY DIFFRACTION100
2.25-2.320.23421610.17352651X-RAY DIFFRACTION100
2.32-2.410.19741270.17192610X-RAY DIFFRACTION100
2.41-2.50.26521260.17062676X-RAY DIFFRACTION99.96
2.5-2.620.21111240.17332647X-RAY DIFFRACTION99.35
2.62-2.760.23551410.17652653X-RAY DIFFRACTION99.54
2.76-2.930.21081380.16992664X-RAY DIFFRACTION99.89
2.93-3.150.20511300.17252687X-RAY DIFFRACTION99.93
3.15-3.470.19571390.16482689X-RAY DIFFRACTION99.96
3.47-3.970.17911460.14422683X-RAY DIFFRACTION99.54
3.97-50.14821600.11912711X-RAY DIFFRACTION99.93
5.01-51.750.20111660.1622831X-RAY DIFFRACTION99.27
Refinement TLS params.Method: refined / Origin x: 0.579291022953 Å / Origin y: 4.23585287473 Å / Origin z: 11.9289567335 Å
111213212223313233
T0.251185450678 Å20.0165471977618 Å2-0.00276114113972 Å2-0.247638071566 Å20.00917784352205 Å2--0.269176835151 Å2
L1.22725123717 °20.032307599506 °2-0.0892539587912 °2-0.629342437375 °20.00666050737526 °2--0.415011201751 °2
S0.0526833039078 Å °-0.0300935695301 Å °-0.0149824581245 Å °0.0270842404521 Å °-0.0525875829118 Å °-0.0502882692493 Å °-0.0238692159237 Å °0.00343799132466 Å °0.000307894982012 Å °
Refinement TLS groupSelection details: all

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