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- PDB-8ujh: X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex... -

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Basic information

Entry
Database: PDB / ID: 8ujh
TitleX-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and a CST1 diglycopeptide.
Components
  • Glycosyl transferaseGlycosyltransferase
  • SAG-related sequence SRS44
KeywordsTRANSFERASE / GT-A fold GalNAc Glycosyltransferase / Mucin-type O-glycosylation / Toxoplasma gondii cyst wall glycosylation
Function / homology
Function and homology information


IgA-specific serine endopeptidase / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / carbohydrate binding / hydrolase activity / Golgi apparatus / membrane
Similarity search - Function
SRS domain / SRS domain / SRS domain superfamily / N-acetylgalactosaminyltransferase / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Lectin domain of ricin B chain profile. ...SRS domain / SRS domain / SRS domain superfamily / N-acetylgalactosaminyltransferase / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Ricin-type beta-trefoil lectin domain / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / 2-acetamido-2-deoxy-beta-D-galactopyranose / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase / SAG-related sequence SRS44
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
Toxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKumar, P. / Samara, N.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)1-ZIA-DE000754-03 United States
CitationJournal: Nat Commun / Year: 2024
Title: A Toxoplasma gondii O-glycosyltransferase that modulates bradyzoite cyst wall rigidity is distinct from host homologues.
Authors: Kumar, P. / Tomita, T. / Gerken, T.A. / Ballard, C.J. / Lee, Y.S. / Weiss, L.M. / Samara, N.L.
History
DepositionOct 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase
C: SAG-related sequence SRS44
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1837
Polymers65,3552
Non-polymers8275
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-19 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.722, 66.833, 166.047
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein / Protein/peptide / Sugars , 3 types, 3 molecules AC

#1: Protein Glycosyl transferase / Glycosyltransferase


Mass: 63514.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_318730 / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: A0A125YMZ8, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide SAG-related sequence SRS44


Mass: 1841.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Toxoplasma gondii (eukaryote)
References: UniProt: S8EZL1, IgA-specific serine endopeptidase
#6: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 23 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1 M CHES pH 9.5 and 14-20% PEG 8000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2022 / Details: FMB OXFORD dual crystal DCM; IDT KB Mirror system
RadiationMonochromator: Double crystal monochromator; liquid nitrogen cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 20609 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.83 Å2 / CC1/2: 0.949 / CC star: 0.987 / Rmerge(I) obs: 0.29 / Rpim(I) all: 0.12 / Rrim(I) all: 0.314 / Net I/σ(I): 7.56
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.557 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 974 / CC1/2: 0.36 / CC star: 0.727 / Rpim(I) all: 0.822 / Rrim(I) all: 1.771 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
Aimlessdata scaling
MOLREPphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→29.74 Å / SU ML: 0.337 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2338 1006 4.89 %
Rwork0.1895 19550 -
obs0.1918 20556 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.18 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 47 19 4313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024431
X-RAY DIFFRACTIONf_angle_d0.51336011
X-RAY DIFFRACTIONf_chiral_restr0.0401623
X-RAY DIFFRACTIONf_plane_restr0.0042782
X-RAY DIFFRACTIONf_dihedral_angle_d13.18281646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.790.31751340.29432672X-RAY DIFFRACTION96.59
2.79-2.960.37981400.28212755X-RAY DIFFRACTION99.9
2.96-3.190.30981300.24582785X-RAY DIFFRACTION100
3.19-3.510.27231420.21722787X-RAY DIFFRACTION99.9
3.51-4.020.22291540.17052770X-RAY DIFFRACTION99.93
4.02-5.060.1781600.13352825X-RAY DIFFRACTION99.9
5.06-29.740.1941460.1682956X-RAY DIFFRACTION99.36
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.154035285270.970171675575-0.317795478562.766019330180.4015722728311.86325843002-0.3549767748320.510230908323-0.264965800848-0.539234747110.1683918758460.23228243235-0.014783605763-0.08933780527070.155905094370.435247310787-0.117108204234-0.03351459420680.3871041474480.002773093680220.295855432577-21.1185546298-17.632050601120.279395744
21.19484756190.8304996191270.1600434790180.7709082433120.06442634395071.62497869652-0.175403126398-0.0097005991277-0.0111410468632-0.07113724107860.05411595908830.192284906875-0.191371152193-0.01449929494150.1305100979960.3752344523390.0138491666434-0.01855420494180.2630754939180.002635860188230.29393140856-15.4072431915-9.4351441111738.3388782103
30.637603914882-0.125754454060.3060876478163.90225800379-3.120375254086.19320381869-0.0935618334326-0.07765157796767.70692578384E-50.3814504951350.07000316764850.0665785542743-0.137035532291-0.03563316305460.03804334702650.3031069002510.0232923961785-0.00282672519260.236217595425-0.03168869115980.261558217173-3.84332614705-16.910587043260.007111317
47.698421688632.57145126714-3.293067310771.18747589177-2.233795403475.320265813240.6416375541960.7359093079530.5928080986810.38449628924-0.136148036836-0.170056627456-0.721277066311-1.16209026287-0.4813990399521.23720735409-0.114177908597-0.009533076167040.9140274814560.03830973752770.505837572188-17.6092822919-20.77693958840.6505007561
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 103 through 286 )AA103 - 2861 - 184
22chain 'A' and (resid 287 through 440 )AA287 - 440185 - 338
33chain 'A' and (resid 441 through 628 )AA441 - 628339 - 526
44chain 'C' and (resid 1 through 7 )CH1 - 71 - 7

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