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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uje
TitleX-ray crystal structure of Toxoplasma gondii GalNAc-T3 in complex with UDP-GalNAc, Mn2+, and Muc5AC-3,13
ComponentsGlycosyl transferase
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
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
: / DI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE / Glycosyl transferase
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 9, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3477
Polymers63,5141
Non-polymers8326
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.409, 65.986, 166.671
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

-
Components

#1: Protein Glycosyl transferase


Mass: 63514.129 Da / Num. of mol.: 1 / Mutation: S297G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_318730 / Plasmid: pPICZ alpha A
Details (production host): His Tag (6x), c-Myc Epitope Tag, TEV protease cleavage site
Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168
References: UniProt: A0A125YMZ8, polypeptide N-acetylgalactosaminyltransferase
#2: Chemical ChemComp-UDP / URIDINE-5'-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
#3: 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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.21 %
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: Apr 1, 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: 2.5→20 Å / Num. obs: 24551 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 52.87 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.072 / Rrim(I) all: 0.164 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 1164 / CC1/2: 0.43 / CC star: 0.775 / Rpim(I) all: 0.598 / Rrim(I) all: 1.127 / % possible all: 96.1

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.20.1_4487refinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.91 Å / SU ML: 0.3409 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2296 1996 8.15 %
Rwork0.1821 22499 -
obs0.186 24495 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4194 0 48 52 4294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224455
X-RAY DIFFRACTIONf_angle_d0.51826047
X-RAY DIFFRACTIONf_chiral_restr0.0409617
X-RAY DIFFRACTIONf_plane_restr0.0045794
X-RAY DIFFRACTIONf_dihedral_angle_d15.01011663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.33521200.28071478X-RAY DIFFRACTION93.18
2.56-2.630.3271600.28291572X-RAY DIFFRACTION99.83
2.63-2.70.3731200.27921609X-RAY DIFFRACTION100
2.7-2.790.34171510.24631563X-RAY DIFFRACTION99.94
2.79-2.890.25761290.23851608X-RAY DIFFRACTION100
2.89-3.010.28251530.23721615X-RAY DIFFRACTION99.94
3.01-3.140.28611360.22191601X-RAY DIFFRACTION100
3.14-3.310.2911430.21331594X-RAY DIFFRACTION99.94
3.31-3.510.26041440.20521599X-RAY DIFFRACTION99.94
3.51-3.780.23321410.18911613X-RAY DIFFRACTION99.94
3.78-4.160.2111470.15541638X-RAY DIFFRACTION99.83
4.16-4.760.1581450.12711626X-RAY DIFFRACTION100
4.76-5.960.19331460.14681648X-RAY DIFFRACTION99.89
5.97-19.910.18851610.1551735X-RAY DIFFRACTION99.63
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)
10.108782805092-0.03364580579110.449150086612.72785767928-2.374551739823.77517057236-0.129900791364-0.0531190874932-0.01263996608040.05882757428930.0431995401694-0.1192234161770.01782680821870.01959103404580.0841945713960.3333971556550.02552979950820.003138091138840.355598056007-0.03935690505820.387783216185-3.09455405837-16.418732001259.1662583758
21.943005303880.726148672870.05760482250483.020143101940.1309392255621.33901959303-0.2319358948650.249639998434-0.0992915698681-0.4542747084290.1355591360380.202835117119-0.08058364711240.03426157726890.09742251119850.430401187149-0.0913909443978-0.05629690701030.5093365452380.004596922350690.3912254115-22.0414894558-15.775475051921.615020496
31.133175213470.1280525286630.5305550654060.21326201127-0.1083303612020.956640636082-0.08104664523590.0199043822464-0.0676887503724-0.0513122301580.0690382982275-0.005797810004930.00796685267057-0.02467472650260.0203058048220.387822393875-0.0310321647966-0.01229170688680.332367938118-0.01047974182550.408645658297-16.06877762-10.618915036839.5188521468
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 429 through 628 )429 - 628327 - 526
22chain 'A' and (resid 103 through 307 )103 - 3071 - 205
33chain 'A' and (resid 308 through 428 )308 - 428206 - 326

+
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