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- PDB-2y8s: Co-structure of an AMA1 mutant (Y230A) with a surface exposed reg... -

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Basic information

Entry
Database: PDB / ID: 2y8s
TitleCo-structure of an AMA1 mutant (Y230A) with a surface exposed region of RON2 from Toxoplasma gondii
Components
  • APICAL MEMBRANE ANTIGEN, PUTATIVE
  • RHOPTRY NECK PROTEIN 2
KeywordsMEMBRANE PROTEIN / MOVING JUNCTION / INVASION
Function / homology
Function and homology information


host cell plasma membrane / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Complement Module; domain 1 - #70 / Apical membrane antigen 1 / Apical membrane antigen 1 / Apical membrane antigen 1 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Complement Module; domain 1 / 3-Layer(bba) Sandwich / Ribbon / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BORIC ACID / Apical membrane antigen 1 / Rhoptry neck protein 2 / Apical membrane antigen 1 / :
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTonkin, M.L. / Roques, M. / Lamarque, M.H. / Pugniere, M. / Douguet, D. / Crawford, J. / Lebrun, M. / Boulanger, M.J.
CitationJournal: Science / Year: 2011
Title: Host Cell Invasion by Apicomplexan Parasites: Insights from the Co-Structure of Ama1 with a Ron2 Peptide
Authors: Tonkin, M.L. / Roques, M. / Lamarque, M.H. / Pugniere, M. / Douguet, D. / Crawford, J. / Lebrun, M. / Boulanger, M.J.
History
DepositionFeb 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APICAL MEMBRANE ANTIGEN, PUTATIVE
B: RHOPTRY NECK PROTEIN 2
D: APICAL MEMBRANE ANTIGEN, PUTATIVE
E: RHOPTRY NECK PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,19211
Polymers103,3494
Non-polymers8427
Water3,801211
1
A: APICAL MEMBRANE ANTIGEN, PUTATIVE
B: RHOPTRY NECK PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2047
Polymers51,6752
Non-polymers5295
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-19 kcal/mol
Surface area18740 Å2
MethodPISA
2
D: APICAL MEMBRANE ANTIGEN, PUTATIVE
E: RHOPTRY NECK PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9884
Polymers51,6752
Non-polymers3132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-21.4 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.520, 96.830, 78.330
Angle α, β, γ (deg.)90.00, 116.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide / Sugars , 3 types, 6 molecules ADBE

#1: Protein APICAL MEMBRANE ANTIGEN, PUTATIVE / AMA1 / APICAL MEMBRANE ANTIGEN 1


Mass: 47921.363 Da / Num. of mol.: 2 / Fragment: DOMAINS I/II/III, RESIDUES 64-484 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: B9QC59, UniProt: B6KAM0*PLUS
#2: Protein/peptide RHOPTRY NECK PROTEIN 2 / RON2


Mass: 3753.281 Da / Num. of mol.: 2 / Fragment: RESIDUES 235-271 / Source method: obtained synthetically / Source: (synth.) TOXOPLASMA GONDII (eukaryote) / References: UniProt: B9QQC1, UniProt: B6KV60*PLUS
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 216 molecules

#4: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 230 TO ALA ENGINEERED RESIDUE IN CHAIN D, TYR 230 TO ALA
Has protein modificationY
Sequence detailsFOR CHAINS B AND E AUTHOR HAS PROVIDED A GENBANK REFERENCE HQ110093.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 % / Description: NONE
Crystal growDetails: 25% PEG 1500, 100 MM MIB PH 4.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→62.97 Å / Num. obs: 30766 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.9
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X2Z

2x2z


Resolution: 2.55→56.7 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.86 / SU B: 10.131 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.958 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26252 1548 5 %RANDOM
Rwork0.18511 ---
obs0.18908 29179 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.105 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.55→56.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6597 0 54 211 6862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226826
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9599259
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0225839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18524.921317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.798151100
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0941530
X-RAY DIFFRACTIONr_chiral_restr0.1130.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215250
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8791.54226
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70226825
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.39732600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0454.52434
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: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 102 -
Rwork0.218 2167 -
obs--99.96 %

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