[English] 日本語
Yorodumi
- PDB-2jh1: Crystal structure of Toxoplasma gondii micronemal protein 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jh1
TitleCrystal structure of Toxoplasma gondii micronemal protein 1
ComponentsMICRONEMAL PROTEIN 1
KeywordsCELL ADHESION / MIC1 / MICRONEME / MAR DOMAIN / CELL INVASION
Function / homology
Function and homology information


symbiont-mediated perturbation of host receptor-mediated signal transduction / effector-mediated perturbation of host innate immune response by symbiont / effector-mediated suppression of host innate immune response / Toll-like receptor 2 binding / microneme / Toll-like receptor 4 binding / host cell surface binding / sialic acid binding / immune system process / host cell endosome ...symbiont-mediated perturbation of host receptor-mediated signal transduction / effector-mediated perturbation of host innate immune response by symbiont / effector-mediated suppression of host innate immune response / Toll-like receptor 2 binding / microneme / Toll-like receptor 4 binding / host cell surface binding / sialic acid binding / immune system process / host cell endosome / cytoplasmic vesicle / carbohydrate binding / cell adhesion
Similarity search - Function
Actin; Chain A, domain 4 - #70 / Micronemal protein 1 / Micronemal protein 1, galectin-like domain / MIC1, C-terminal superfamily / Toxoplasma gondii micronemal protein 1 TgMIC1 / Micronemal adhesive repeat, sialic-acid binding / Sialic-acid binding micronemal adhesive repeat / Actin; Chain A, domain 4 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Micronemal protein 1
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsBlumenschein, T.M.A. / Friedrich, N. / Childs, R.A. / Saouros, S. / Carpenter, E.P. / Campanero-Rhodes, M.A. / Simpson, P. / Koutroukides, T. / Blackman, M.J. / Feizi, T. ...Blumenschein, T.M.A. / Friedrich, N. / Childs, R.A. / Saouros, S. / Carpenter, E.P. / Campanero-Rhodes, M.A. / Simpson, P. / Koutroukides, T. / Blackman, M.J. / Feizi, T. / Soldati-Favre, D. / Matthews, S.
CitationJournal: Embo J. / Year: 2007
Title: Atomic Resolution Insight Into Host Cell Recognition by Toxoplasma Gondii.
Authors: Blumenschein, T.M.A. / Friedrich, N. / Childs, R.A. / Saouros, S. / Carpenter, E.P. / Campanero-Rhodes, M.A. / Simpson, P. / Chai, W. / Koutroukides, T. / Blackman, M.J. / Feizi, T. / ...Authors: Blumenschein, T.M.A. / Friedrich, N. / Childs, R.A. / Saouros, S. / Carpenter, E.P. / Campanero-Rhodes, M.A. / Simpson, P. / Chai, W. / Koutroukides, T. / Blackman, M.J. / Feizi, T. / Soldati-Favre, D. / Matthews, S.
History
DepositionFeb 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn / struct_conn_type
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MICRONEMAL PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,31320
Polymers27,1721
Non-polymers1,14119
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.192, 66.192, 172.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2046-

HOH

21A-2047-

HOH

31A-2080-

HOH

41A-2081-

HOH

-
Components

#1: Protein MICRONEMAL PROTEIN 1 / MIC1


Mass: 27172.219 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 17-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI DE3 / References: UniProt: O00834
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.6 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.6
Details: VAPOUR DIFFUSION, HANGING DROP 3.6 M AMMONIUM ACETATE, 100 MM BIS-TRIS-PROPANE PH 7.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 26, 2006 / Details: COLLIMATOR, MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→18 Å / Num. obs: 30153 / % possible obs: 96.6 % / Observed criterion σ(I): -3.7 / Redundancy: 5.1 % / Rsym value: 0.08 / Net I/σ(I): 19.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.31 / % possible all: 76.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→17.49 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.63 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS DENSITY ON A TWO FOLD AXIS ADJACENT TO RESIDUE 111 WHICH COULD BE DUE TO A PARTIALLY DISORDERED GLYCEROL MOLECULE.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1525 5.1 %RANDOM
Rwork0.178 ---
obs0.179 28518 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.77 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→17.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 74 181 2042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211952
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9632646
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6535256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90723.73691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60615315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.271517
X-RAY DIFFRACTIONr_chiral_restr0.1160.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021551
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2902
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21304
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2175
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2106
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0991.51274
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73521965
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8753760
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4444.5669
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.313 77
Rwork0.294 1585

+
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