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

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Basic information

Entry
Database: PDB / ID: 8ujf
TitleX-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and Muc5AC-3,13
Components
  • Glycosyl transferase
  • Mucin-5AC
KeywordsTRANSFERASE / GT-A fold GalNAc Glycosyltransferase / Mucin-type O-glycosylation / Toxoplasma gondii cyst wall glycosylation
Function / homology
Function and homology information


mucus layer / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / protein O-linked glycosylation / extracellular matrix structural constituent ...mucus layer / polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / protein O-linked glycosylation / extracellular matrix structural constituent / Dectin-2 family / extracellular matrix / Golgi lumen / carbohydrate binding / Golgi membrane / nucleotide binding / extracellular space / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
N-acetylgalactosaminyltransferase / WxxW domain / Mucin-2 protein WxxW repeating region / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain ...N-acetylgalactosaminyltransferase / WxxW domain / Mucin-2 protein WxxW repeating region / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / : / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot signature. / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / Glycosyltransferase 2-like / Glycosyl transferase family 2 / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / 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
: / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase / Mucin-5AC
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferase
B: Glycosyl transferase
E: Mucin-5AC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,77910
Polymers128,5303
Non-polymers1,2497
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.233, 123.693, 165.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 103 through 137 or resid 139...
d_2ens_1(chain "B" and (resid 103 through 137 or resid 139...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUPROA1 - 35
d_12ens_1ALAILEA37 - 162
d_13ens_1ALAGLYA164 - 216
d_14ens_1CYSGLNA218 - 235
d_15ens_1ALAGLYA237 - 273
d_16ens_1TYRPROA275 - 350
d_17ens_1SERMETA352 - 400
d_18ens_1LEUVALA402 - 517
d_21ens_1GLUPROB2 - 36
d_22ens_1ALAILEB38 - 163
d_23ens_1ALAGLNB165 - 235
d_24ens_1ALAGLYB237 - 273
d_25ens_1TYRLYSB275 - 314
d_26ens_1PROPROB322 - 357
d_27ens_1SERMETB359 - 407
d_28ens_1LEUVALB409 - 524

NCS oper: (Code: givenMatrix: (0.99971071173, 0.0205682878425, 0.0124674931939), (0.0202552169266, -0.999488759356, 0.0247375445113), (0.0129699282407, -0.0244778564507, -0.999616234114)Vector: 33. ...NCS oper: (Code: given
Matrix: (0.99971071173, 0.0205682878425, 0.0124674931939), (0.0202552169266, -0.999488759356, 0.0247375445113), (0.0129699282407, -0.0244778564507, -0.999616234114)
Vector: 33.1913742985, -0.457701041498, 1.13240433964)

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Components

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Protein / Protein/peptide / Sugars , 3 types, 4 molecules ABE

#1: Protein Glycosyl transferase


Mass: 63514.129 Da / Num. of mol.: 2
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 Mucin-5AC / MUC-5AC / Gastric mucin / Major airway glycoprotein / Mucin-5 subtype AC / tracheobronchial / ...MUC-5AC / Gastric mucin / Major airway glycoprotein / Mucin-5 subtype AC / tracheobronchial / Tracheobronchial mucin / TBM


Mass: 1501.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P98088
#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 natural source / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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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Non-polymers , 3 types, 30 molecules

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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.7 Å3/Da / Density % sol: 54.53 %
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-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 1, 2022 / Details: CRL single axis focusing system
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→20.01 Å / Num. obs: 30811 / % possible obs: 97.2 % / Redundancy: 6 % / Biso Wilson estimate: 50.33 Å2 / CC1/2: 0.95 / CC star: 0.987 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.136 / Rrim(I) all: 0.324 / Net I/σ(I): 5
Reflection shellResolution: 2.87→2.9 Å / Rmerge(I) obs: 1.568 / Mean I/σ(I) obs: 0.87 / Num. unique obs: 1402 / CC1/2: 0.377 / CC star: 0.74 / Rpim(I) all: 0.697 / Rrim(I) all: 1.723 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUIdata collection
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→20.01 Å / SU ML: 0.4617 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.2115
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2741 1998 6.51 %
Rwork0.2173 28704 -
obs0.221 30702 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.88 Å2
Refinement stepCycle: LAST / Resolution: 2.87→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8345 0 68 24 8437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00338692
X-RAY DIFFRACTIONf_angle_d0.640811795
X-RAY DIFFRACTIONf_chiral_restr0.04431218
X-RAY DIFFRACTIONf_plane_restr0.00921538
X-RAY DIFFRACTIONf_dihedral_angle_d15.16813226
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.877118631989 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-2.940.32451270.31261818X-RAY DIFFRACTION88.73
2.94-3.020.38351340.31251940X-RAY DIFFRACTION91.57
3.02-3.110.39171340.29231925X-RAY DIFFRACTION92.92
3.11-3.210.35831340.28551946X-RAY DIFFRACTION94.25
3.21-3.330.32961420.26912025X-RAY DIFFRACTION95.55
3.33-3.460.34181400.27472034X-RAY DIFFRACTION97.36
3.46-3.620.3271440.24592058X-RAY DIFFRACTION98.61
3.62-3.810.28131450.22982082X-RAY DIFFRACTION98.85
3.81-4.040.24841460.19872100X-RAY DIFFRACTION99.65
4.04-4.350.22861470.17012117X-RAY DIFFRACTION100
4.35-4.780.22651490.1632137X-RAY DIFFRACTION99.96
4.78-5.460.22031490.17422142X-RAY DIFFRACTION100
5.46-6.840.27151500.20682160X-RAY DIFFRACTION99.83
6.84-20.010.21681570.18322220X-RAY DIFFRACTION97.98
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)
11.15570854687-0.3312376805741.06622829761.25251146685-0.609532952160.4859976325030.1145418783550.4399232201120.118761385127-0.263598595683-0.1515109457330.1024891743510.2688410243240.2667720567510.04570989669790.5140782230930.11024024248-0.03211671991930.491482307746-0.01160448779710.27374173579417.249855200121.3876831706-19.6851767637
20.603008161450.1067941852340.1182517282120.254721116835-0.4470369438970.681393615233-0.04303500911120.455771921536-0.08791400205360.07696659997830.0311410370469-0.0605875534961-0.0825910611022-0.207026724009-0.02299364674760.3668464650390.00467930785790.02453438200340.248579080688-0.006427873696410.30458194423823.131151589116.1752776529-1.22417187366
31.49218647319-0.149929366158-1.454703434190.172509090354-0.7329754758571.451038869990.0383654831912-0.030952917484-0.276821425980.0122222060739-0.1426150636910.0755329285885-0.159076344046-0.06617638018490.04854046798630.222644875816-0.0539664797949-0.05773342635290.311364084547-0.05690392473280.37484811160816.72674127523.1834321934818.2311807804
41.036836257490.5045566770530.2056209940792.424459695640.3445296651180.6311641388980.0739031421711-0.0286616916218-0.01562946690020.156674153112-0.228373813066-0.0344171026291-0.0275687768432-0.02281558990020.1177246805910.261608488896-0.0298301278783-0.02557665921890.1576322485030.0244627670140.28701637118350.1226914181-22.222784905319.34467211
50.567698777552-0.4713148987790.8528720774010.626391828517-0.5053800854341.411413750770.00800524247840.129298482167-0.0283337561306-0.0537045574415-0.047456611698-0.0290799429804-0.1005130486480.1483468148870.03348781761930.26222663948-0.06151782433720.04752500100630.373585163388-0.001622704195580.37126351592452.5237723749-6.73718816987-10.2316617301
60.645783040633-0.58421325712-1.510953933020.5279163571441.365688722513.53247177686-0.1765660143860.183116787168-0.313486529056-0.4292864600860.275552240951-0.5917994972680.1929006283310.470167743498-0.2450245504651.142791492680.602198534589-0.03375750600811.32970721883-0.5444934909960.72806194279946.3189799179-22.1270310355-2.77905828563
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 307 )AA103 - 3071 - 205
22chain 'A' and (resid 308 through 428 )AA308 - 428206 - 317
33chain 'A' and (resid 429 through 628 )AA429 - 628318 - 517
44chain 'B' and (resid 102 through 323 )BB102 - 3231 - 219
55chain 'B' and (resid 324 through 628 )BB324 - 628220 - 524
66chain 'E' and (resid 4 through 6 )EI4 - 61 - 3

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