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- PDB-9n3s: Crystal structure of the fungal mannosyltransferase Och1 reveals ... -

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Basic information

Entry
Database: PDB / ID: 9n3s
TitleCrystal structure of the fungal mannosyltransferase Och1 reveals active site primed for N-glycan binding
ComponentsInitiation-specific alpha-1,6-mannosyltransferase
KeywordsTRANSFERASE / cis-Golgi apparatus
Function / homology
Function and homology information


initiation-specific alpha-1,6-mannosyltransferase / alpha-1,6-mannosyltransferase activity / mannan polymerase complex / initiation-specific glycolipid 1,6-alpha-mannosyltransferase activity / Golgi cis cisterna / protein N-linked glycosylation / endoplasmic reticulum membrane
Similarity search - Function
Initiation-specific alpha-1,6-mannosyltransferase Och1-like / Glycosyltransferase, DXD sugar-binding motif / Glycosyltransferase sugar-binding region containing DXD motif / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Initiation-specific alpha-1,6-mannosyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKelly, E.T.R. / Rodionov, D. / Berghuis, A.M.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-114889 Canada
Canadian Institutes of Health Research (CIHR)PJT-162365 Canada
CitationJournal: Plos One / Year: 2025
Title: Crystal structure of the fungal mannosyltransferase Och1 reveals active site primed for N-glycan binding.
Authors: Kelly, E.T.R. / Rodionov, D. / Sleno, B. / Romero, P.A. / Berghuis, A.M.
History
DepositionJan 31, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 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: Initiation-specific alpha-1,6-mannosyltransferase
B: Initiation-specific alpha-1,6-mannosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2866
Polymers98,9812
Non-polymers2,3054
Water4,053225
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A: Initiation-specific alpha-1,6-mannosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1503
Polymers49,4911
Non-polymers1,6602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Initiation-specific alpha-1,6-mannosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1363
Polymers49,4911
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.447, 57.090, 84.088
Angle α, β, γ (deg.)85.57, 75.31, 75.13
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

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Protein / Non-polymers , 2 types, 227 molecules AB

#1: Protein Initiation-specific alpha-1,6-mannosyltransferase / Outer chain elongation protein 1


Mass: 49490.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OCH1, NGD29, YGL038C / Production host: Komagataella pastoris (fungus)
References: UniProt: P31755, initiation-specific alpha-1,6-mannosyltransferase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Komagataella pastoris (fungus)
References: initiation-specific alpha-1,6-mannosyltransferase
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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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: 1.97 Å3/Da / Density % sol: 37.56 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 Bis-TRIS pH 6.5, 25% PEG 3350, 30 mM NaF

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Data collection

DiffractionMean temperature: 228.15 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→24.46 Å / Num. obs: 44906 / % possible obs: 89.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 30.75 Å2 / Net I/σ(I): 4.81
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.34 / % possible all: 58.2

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Processing

Software
NameVersionClassification
PHENIXDEV_4694refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→24.46 Å / SU ML: 0.199 / Cross valid method: FREE R-VALUE / σ(F): 1.79 / Phase error: 26.72
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.243 1999 4.45 %
Rwork0.198 --
obs0.2 44906 89.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.52 Å2
Refinement stepCycle: LAST / Resolution: 2.01→24.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5812 0 153 225 6190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086116
X-RAY DIFFRACTIONf_angle_d0.9368327
X-RAY DIFFRACTIONf_dihedral_angle_d6.549861
X-RAY DIFFRACTIONf_chiral_restr0.058960
X-RAY DIFFRACTIONf_plane_restr0.0081048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.2461890.21772015X-RAY DIFFRACTION58
2.06-2.120.23711260.20432552X-RAY DIFFRACTION76
2.12-2.180.27881240.20822782X-RAY DIFFRACTION81
2.18-2.250.24351470.21333037X-RAY DIFFRACTION89
2.25-2.330.25911550.21813186X-RAY DIFFRACTION93
2.33-2.430.29871490.24343250X-RAY DIFFRACTION94
2.43-2.540.30891480.24583209X-RAY DIFFRACTION95
2.54-2.670.30591510.25293228X-RAY DIFFRACTION94
2.67-2.840.33941480.25773161X-RAY DIFFRACTION93
2.84-3.060.29751430.25173154X-RAY DIFFRACTION93
3.06-3.360.29191550.20633344X-RAY DIFFRACTION96
3.36-3.850.20011510.16463301X-RAY DIFFRACTION97
3.85-4.840.18831540.14713335X-RAY DIFFRACTION98
4.84-24.460.18221590.16973353X-RAY DIFFRACTION98

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