[English] 日本語
Yorodumi
- PDB-8ujg: X-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ujg
TitleX-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and the mono-glycopeptide Srs13.2
Components
  • Glycosyl transferase
  • SAG-related sequence SRS13
KeywordsTRANSFERASE / GT-A fold GalNAc Glycosyltransferase / Mucin-type O-glycosylation / Toxoplasma gondii cyst wall glycosylation
Function / homology
Function and homology information


polypeptide N-acetylgalactosaminyltransferase / polypeptide N-acetylgalactosaminyltransferase activity / protein O-linked glycosylation / carbohydrate binding / Golgi membrane / nucleotide binding / metal ion binding
Similarity search - Function
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-alpha-D-galactopyranose / : / DI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase / SAG-related sequence SRS13
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
Toxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyl transferase
B: Glycosyl transferase
D: SAG-related sequence SRS13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,38122
Polymers128,9983
Non-polymers2,38219
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.614, 122.624, 165.655
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 99 through 141 or resid 143...
d_2ens_1(chain "B" and (resid 99 through 141 or resid 143...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUALAALAAA99 - 14127 - 69
d_12GLYGLYARGARGAA143 - 15871 - 86
d_13ALAALAHISHISAA160 - 20088 - 128
d_14VALVALVALVALAA202130
d_15ASNASNPROPROAA204 - 208132 - 136
d_16ILEILEGLUGLUAA210 - 213138 - 141
d_17ILEILELEULEUAA215 - 234143 - 162
d_18GLUGLUGLUGLUAA236 - 251164 - 179
d_19ARGARGILEILEAA253 - 264181 - 192
d_110ALAALAVALVALAA266 - 301194 - 229
d_111PROPROPHEPHEAA303 - 313231 - 241
d_112HISHISHISHISAA315 - 333243 - 261
d_113TYRTYRASPASPAA335 - 375263 - 303
d_114GLYGLYPHEPHEAA377 - 385305 - 313
d_115GLYGLYSERSERAA387 - 421315 - 349
d_116PROPROTHRTHRAA426 - 437354 - 365
d_117LEULEUARGARGAA439 - 456367 - 384
d_118ASNASNARGARGAA458 - 471386 - 399
d_119ARGARGMETMETAA473 - 511401 - 439
d_120LEULEUGLNGLNAA513 - 536441 - 464
d_121PHEPHELYSLYSAA538 - 543466 - 471
d_122GLYGLYPROPROAA545 - 549473 - 477
d_123ASNASNVALVALAA551 - 628479 - 556
d_21LEULEUALAALABB99 - 14127 - 69
d_22GLYGLYARGARGBB143 - 15871 - 86
d_23ALAALAHISHISBB160 - 20088 - 128
d_24VALVALVALVALBB202130
d_25ASNASNPROPROBB204 - 208132 - 136
d_26ILEILEGLUGLUBB210 - 213138 - 141
d_27ILEILELEULEUBB215 - 234143 - 162
d_28GLUGLUGLUGLUBB236 - 251164 - 179
d_29ARGARGILEILEBB253 - 264181 - 192
d_210ALAALAVALVALBB266 - 301194 - 229
d_211PROPROPHEPHEBB303 - 313231 - 241
d_212HISHISHISHISBB315 - 333243 - 261
d_213TYRTYRASPASPBB335 - 375263 - 303
d_214GLYGLYPHEPHEBB377 - 385305 - 313
d_215GLYGLYTHRTHRBB387 - 437315 - 365
d_216LEULEUARGARGBB439 - 456367 - 384
d_217ASNASNARGARGBB458 - 471386 - 399
d_218ARGARGMETMETBB473 - 511401 - 439
d_219LEULEUGLNGLNBB513 - 536441 - 464
d_220PHEPHELYSLYSBB538 - 543466 - 471
d_221GLYGLYPROPROBB545 - 549473 - 477
d_222ASNASNVALVALBB551 - 628479 - 556

NCS oper: (Code: givenMatrix: (0.998804961332, -0.0427503709905, -0.0236865995529), (-0.0436072743762, -0.998366121128, -0.0369255170031), (-0.0220693189674, 0.0379142976282, -0.999037262166)Vector: ...NCS oper: (Code: given
Matrix: (0.998804961332, -0.0427503709905, -0.0236865995529), (-0.0436072743762, -0.998366121128, -0.0369255170031), (-0.0220693189674, 0.0379142976282, -0.999037262166)
Vector: 33.3503523194, -0.711200804321, -2.19157143008)

-
Components

-
Protein / Protein/peptide / Sugars , 3 types, 4 molecules ABD

#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 / Plasmid: pPICz-alpha
Details (production host): His Tag (6x), c-Myc Epitope Tag, TEV protease site
Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: A0A125YMZ8, polypeptide N-acetylgalactosaminyltransferase
#2: Protein/peptide SAG-related sequence SRS13


Mass: 1970.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Toxoplasma gondii (eukaryote) / References: UniProt: S8F856
#7: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


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

-
Non-polymers , 5 types, 259 molecules

#3: 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
#4: 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
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.82 %
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)

-
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: Oct 28, 2022 / Details: CRL single axis focusing system
RadiationMonochromator: FMB OXFORD single crystal side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→30 Å / Num. obs: 62158 / % possible obs: 99.5 % / Redundancy: 7 % / Biso Wilson estimate: 38.55 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.081 / Rrim(I) all: 0.216 / Net I/σ(I): 12
Reflection shellResolution: 2.27→2.34 Å / Rmerge(I) obs: 1.647 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3034 / CC1/2: 0.504 / CC star: 0.818 / Rpim(I) all: 0.682 / Rrim(I) all: 1.787 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SERGUI1.20.1_4487data collection
Aimlessdata scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→29.66 Å / SU ML: 0.3093 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.1194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2369 3121 5.03 %
Rwork0.1923 58919 -
obs0.1945 62040 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.39 Å2
Refinement stepCycle: LAST / Resolution: 2.27→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8460 0 142 241 8843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00289021
X-RAY DIFFRACTIONf_angle_d0.601312249
X-RAY DIFFRACTIONf_chiral_restr0.04241267
X-RAY DIFFRACTIONf_plane_restr0.00811596
X-RAY DIFFRACTIONf_dihedral_angle_d14.35293352
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.817553700325 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.310.3336960.29751936X-RAY DIFFRACTION71.83
2.31-2.350.3441530.28112665X-RAY DIFFRACTION99.89
2.35-2.390.30221300.2732701X-RAY DIFFRACTION99.68
2.39-2.430.3111400.26132686X-RAY DIFFRACTION99.96
2.43-2.480.33411560.25042699X-RAY DIFFRACTION99.86
2.48-2.530.25941500.25792644X-RAY DIFFRACTION99.96
2.53-2.580.3161460.25232715X-RAY DIFFRACTION99.76
2.58-2.640.31511330.23852693X-RAY DIFFRACTION99.93
2.64-2.710.3071490.23962688X-RAY DIFFRACTION100
2.71-2.780.26391250.22112745X-RAY DIFFRACTION99.97
2.78-2.860.26741530.21352628X-RAY DIFFRACTION98.62
2.86-2.960.27531480.22262695X-RAY DIFFRACTION99.27
2.96-3.060.24711460.21912699X-RAY DIFFRACTION99.96
3.06-3.190.33261530.21732731X-RAY DIFFRACTION99.86
3.19-3.330.27751470.19882724X-RAY DIFFRACTION99.9
3.33-3.510.26491450.19812715X-RAY DIFFRACTION99.9
3.51-3.720.22961300.18872737X-RAY DIFFRACTION99.79
3.72-4.010.18451360.15852729X-RAY DIFFRACTION99.51
4.01-4.410.16141420.1352693X-RAY DIFFRACTION97.42
4.41-5.050.17611350.13112764X-RAY DIFFRACTION99.52
5.05-6.350.1861560.1652792X-RAY DIFFRACTION99.43
6.35-29.660.19721520.18252840X-RAY DIFFRACTION96.89
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)
11.93823130251-0.533982956578-0.07483311697862.491773143810.2135980173631.734813670560.10742540360.3653665717860.0573108424861-0.281022004233-0.2622446694410.1039133648210.002354742274860.005308308395380.1445956164940.297753878450.07281799966670.004730622635930.3094717304710.02741207091230.296006670596-17.465356242521.8042531057-21.8464507032
20.182618022889-0.20672805956-0.08208402572280.997969672934-0.3495410023491.445122163640.0312870115053-0.03907618369740.06461385148260.0546961861123-0.106064308915-0.1510257561210.03184256586170.1270890282940.08217480471350.222267567120.00398969541303-0.01155874423050.2968629688910.03292791258950.324002362645-9.0902361853616.7038710077-3.84409725324
31.656102513430.162346997649-1.022469537630.562599366144-0.7092535504592.5923788337-0.00989612789121-0.3073990671530.04259650209930.00676302489675-0.119829543363-0.04299072932990.175765814380.1860702071070.1075978122970.2876811791680.00750082546681-0.03768882501870.3204195032390.005811926731670.317251052816-16.44914468392.6781493909516.2362751255
41.652959150940.260212300522-0.4465569895860.676156148699-0.7058004459581.300292912470.141362973354-0.3359757262550.01855628463260.190499190123-0.197765688663-0.000760548605461-0.04811631213580.1809548099530.04658617289640.406106354011-0.08514424245770.02734691828130.301283411732-0.01682069412920.27434905090819.3302962974-19.414541010913.6586885169
51.187916941-0.4122690707850.6654377303170.160418885653-0.9186354166211.957966952890.03787805469760.0430992177090.188946169857-0.0497774405215-0.100566249566-0.01034659999550.133450759526-0.02639894871710.04724242913020.2381437500280.000216547234310.01537787695490.254840080157-0.03011930448220.30401762774316.5033049121-4.27321310455-15.9846917959
62.384931696493.106790945691.712820480624.047124022172.201573024015.210064900990.220640873781-0.4511044986250.09864553573540.454601187216-0.1955785192690.07362189178550.01294167299060.0699434205168-0.006117266815011.11940048161-0.2739242745920.1618918352990.8246627214740.03913178307971.11029605819-20.384616131817.8900806509-0.486159272805
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 99 through 286 )AA99 - 2861 - 188
22chain 'A' and (resid 287 through 428 )AA287 - 428189 - 330
33chain 'A' and (resid 429 through 628 )AA429 - 628331 - 530
44chain 'B' and (resid 98 through 402 )BB98 - 4021 - 305
55chain 'B' and (resid 403 through 635 )BB403 - 635306 - 530
66chain 'D' and (resid 2 through 3 )DH2 - 31 - 2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more