[English] 日本語
Yorodumi
- PDB-1ynt: Structure of the monomeric form of T. gondii SAG1 surface antigen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ynt
TitleStructure of the monomeric form of T. gondii SAG1 surface antigen bound to a human Fab
Components
  • 4F11E12 Fab variable heavy chain region
  • 4F11E12 Fab variable light chain region
  • Major surface antigen p30
  • protein L
KeywordsIMMUNE SYSTEM / Toxoplasma gondii / recombinant SAG1 / conformational epitope
Function / homology
Function and homology information


symbiont-containing vacuole / IgG binding / immunoglobulin binding / membrane
Similarity search - Function
SRS domain / Protozoan surface antigen, SAG1 family / SRS domain / SRS domain / SRS domain superfamily / Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding ...SRS domain / Protozoan surface antigen, SAG1 family / SRS domain / SRS domain / SRS domain superfamily / Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Major surface antigen p30 / Protein L
Similarity search - Component
Biological speciesFinegoldia magna (bacteria)
Toxoplasma gondii (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGraille, M. / Stura, E.A. / Bossus, M. / Muller, B.H. / Letourneur, O. / Battail-Poirot, N. / Sibai, G. / Rolland, D. / Le Du, M.H. / Ducancel, F.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of the complex between the monomeric form of Toxoplasma gondii surface antigen 1 (SAG1) and a monoclonal antibody that mimics the human immune response
Authors: Graille, M. / Stura, E.A. / Bossus, M. / Muller, B.H. / Letourneur, O. / Battail-Poirot, N. / Sibai, G. / Gauthier, M. / Rolland, D. / Le Du, M.H. / Ducancel, F.
History
DepositionJan 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 3, 2018Group: Structure summary / Category: audit_author / struct / Item: _audit_author.name / _struct.title
Revision 1.5Dec 4, 2019Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.6Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4F11E12 Fab variable light chain region
B: 4F11E12 Fab variable heavy chain region
C: 4F11E12 Fab variable light chain region
D: 4F11E12 Fab variable heavy chain region
E: protein L
F: Major surface antigen p30
G: Major surface antigen p30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5489
Polymers154,3237
Non-polymers2252
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.034, 198.285, 128.366
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a Fab - antigen complex. Two are present in the asymetric unit

-
Components

#1: Antibody 4F11E12 Fab variable light chain region


Mass: 23577.820 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody 4F11E12 Fab variable heavy chain region


Mass: 23568.344 Da / Num. of mol.: 2 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein protein L /


Mass: 6750.485 Da / Num. of mol.: 1 / Fragment: domain C*
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM103 / References: UniProt: Q51918*PLUS
#4: Protein Major surface antigen p30 / SAG1 protein


Mass: 26640.217 Da / Num. of mol.: 2 / Fragment: residues in database 50-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pTG8639 / Production host: Pichia pastoris (fungus) / References: UniProt: P13664
#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 57.985123 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 11
Details: 15% polyethylene glycol 3350, 0.25M NaCl, 150mM CAPS, pH 11, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 29, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 32176 / Num. obs: 31886 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 / Χ2: 1.241
Reflection shellResolution: 3.1→3.19 Å / Rmerge(I) obs: 0.497 / Num. unique all: 2608 / Χ2: 0.866 / % possible all: 97.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.501data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB codes: 1F11, 1KB5, 1KZQ

1f11

1kb5

1kzq


Resolution: 3.1→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.283 1534 4.8 %
Rwork0.241 --
all-30981 -
obs-30981 96.7 %
Displacement parametersBiso mean: 10 Å2
Baniso -1Baniso -2Baniso -3
1--11.613 Å20 Å20 Å2
2---9.251 Å20 Å2
3---20.864 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10800 0 2 0 10802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.535

+
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