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- PDB-2jh7: Crystal structure of Toxoplasma gondii micronemal protein 1 bound... -

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Basic information

Entry
Database: PDB / ID: 2jh7
TitleCrystal structure of Toxoplasma gondii micronemal protein 1 bound to 6'-sialyl-N-acetyllactosamine
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 / MOLECULAR REPLACEMENT / Resolution: 2.07 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 20, 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 1.3May 8, 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_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MICRONEMAL PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,76019
Polymers27,2661
Non-polymers1,49418
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)65.935, 65.935, 172.983
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-2020-

HOH

21A-2050-

HOH

31A-2051-

HOH

41A-2083-

HOH

51A-2084-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein MICRONEMAL PROTEIN 1 / MIC1


Mass: 27266.010 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: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 198 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


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


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


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

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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: 3.46 Å3/Da / Density % sol: 64.6 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.8
Details: VAPOUR DIFFUSION IN HANGING DROP 3.6M AMMONIUM ACETATE 100 MM BIS-TRIS-PROPANE PH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 29, 2006 / Details: COLLIMATOR, MONOCHROMATOR, MIRROR
RadiationMonochromator: ASSYMETRIC CUT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 49275 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 7.6 % / Rsym value: 0.11 / Net I/σ(I): 43.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 6.7 / Rsym value: 0.54 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JH1

2jh1


Resolution: 2.07→18.29 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.856 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.133 / 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
Rfree0.212 1218 5.1 %RANDOM
Rwork0.183 ---
obs0.184 22744 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.07→18.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 98 181 2003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211874
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.9852536
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76323.53782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25815294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1491516
X-RAY DIFFRACTIONr_chiral_restr0.1240.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021451
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.2772
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21249
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2741.51213
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92421862
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0013748
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5644.5671
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: 2.07→2.12 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.356 83
Rwork0.284 1632

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