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- PDB-4yiz: Crystal structure of engineered TgAMA1 lacking the DII loop in co... -

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Basic information

Entry
Database: PDB / ID: 4yiz
TitleCrystal structure of engineered TgAMA1 lacking the DII loop in complex with an Eimeria tenella RON2D3 peptide
Components
  • Apical membrane antigen AMA1
  • Rhoptry neck protein 2, putative
KeywordsIMMUNE SYSTEM / Apicomplexa / invasion / moving junction / parasite / protein engineering / PAN domain
Function / homology
Function and homology information


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
2-acetamido-2-deoxy-alpha-D-galactopyranose / Apical membrane antigen AMA1 / Rhoptry neck protein 2, putative
Similarity search - Component
Biological speciesToxoplasma gondii ME49 (eukaryote)
Eimeria tenella (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsParker, M.L. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP82915 Canada
CitationJournal: Plos One / Year: 2015
Title: An Extended Surface Loop on Toxoplasma gondii Apical Membrane Antigen 1 (AMA1) Governs Ligand Binding Selectivity.
Authors: Parker, M.L. / Boulanger, M.J.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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 2.2Oct 30, 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 AMA1
C: Apical membrane antigen AMA1
E: Apical membrane antigen AMA1
B: Rhoptry neck protein 2, putative
D: Rhoptry neck protein 2, putative
F: Rhoptry neck protein 2, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,17515
Polymers149,8106
Non-polymers1,3659
Water8,773487
1
A: Apical membrane antigen AMA1
B: Rhoptry neck protein 2, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5716
Polymers49,9372
Non-polymers6354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-39 kcal/mol
Surface area19480 Å2
MethodPISA
2
C: Apical membrane antigen AMA1
D: Rhoptry neck protein 2, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3505
Polymers49,9372
Non-polymers4133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-32 kcal/mol
Surface area19510 Å2
MethodPISA
3
E: Apical membrane antigen AMA1
F: Rhoptry neck protein 2, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2544
Polymers49,9372
Non-polymers3172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-33 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.928, 265.928, 94.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-503-

SO4

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ACEBDF

#1: Protein Apical membrane antigen AMA1


Mass: 46064.297 Da / Num. of mol.: 3 / Fragment: residues 64-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii ME49 (eukaryote) / Gene: TGME49_255260 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: S8GKS3
#2: Protein/peptide Rhoptry neck protein 2, putative


Mass: 3872.359 Da / Num. of mol.: 3 / Fragment: residues 1261-1285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eimeria tenella (eukaryote) / Gene: ETH_00012760 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U6KQJ2

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Sugars , 2 types, 4 molecules

#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.: 3
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
#4: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 492 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsThe authors state that the twenty flexible residues of the DII loop (HTYPLTSQASWNDWWPLHQS) were ...The authors state that the twenty flexible residues of the DII loop (HTYPLTSQASWNDWWPLHQS) were replaced with a seven residue Gly-Ser linker (GSGSGSG).

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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: 6.42 Å3/Da / Density % sol: 80.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M tri-sodium citrate pH 5.0 and 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2013
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→72.89 Å / Num. obs: 180412 / % possible obs: 93.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.6
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.4 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2Y8T

2y8t


Resolution: 2.2→59.5 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.207 9059 5.03 %Random selection
Rwork0.187 ---
obs0.188 179956 93.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.95 Å2
Refinement stepCycle: LAST / Resolution: 2.2→59.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9975 0 81 487 10543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310421
X-RAY DIFFRACTIONf_angle_d0.84514134
X-RAY DIFFRACTIONf_dihedral_angle_d14.383858
X-RAY DIFFRACTIONf_chiral_restr0.0321515
X-RAY DIFFRACTIONf_plane_restr0.0031880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.23423050.23685676X-RAY DIFFRACTION94
2.225-2.25120.36192670.365632X-RAY DIFFRACTION92
2.2512-2.27870.28743050.26945697X-RAY DIFFRACTION94
2.2787-2.30750.24623180.21885593X-RAY DIFFRACTION92
2.3075-2.33790.23952760.21845720X-RAY DIFFRACTION94
2.3379-2.36990.2663260.21815779X-RAY DIFFRACTION95
2.3699-2.40380.24952590.21075831X-RAY DIFFRACTION96
2.4038-2.43960.22713190.20265849X-RAY DIFFRACTION96
2.4396-2.47780.21333240.19935775X-RAY DIFFRACTION95
2.4778-2.51840.23773080.20795727X-RAY DIFFRACTION95
2.5184-2.56180.24522900.21165633X-RAY DIFFRACTION92
2.5618-2.60840.24273190.2125554X-RAY DIFFRACTION92
2.6084-2.65860.24572650.21245022X-RAY DIFFRACTION83
2.6586-2.71280.23423000.21675653X-RAY DIFFRACTION93
2.7128-2.77180.20463060.2045910X-RAY DIFFRACTION97
2.7718-2.83630.23452910.21025892X-RAY DIFFRACTION97
2.8363-2.90720.23432870.21135698X-RAY DIFFRACTION94
2.9072-2.98580.24422900.21635795X-RAY DIFFRACTION95
2.9858-3.07370.22993230.20455828X-RAY DIFFRACTION96
3.0737-3.17290.2422990.19925802X-RAY DIFFRACTION95
3.1729-3.28630.22433170.19755824X-RAY DIFFRACTION96
3.2863-3.41780.22722910.18595404X-RAY DIFFRACTION89
3.4178-3.57340.19332840.17435475X-RAY DIFFRACTION89
3.5734-3.76170.16953280.15565962X-RAY DIFFRACTION97
3.7617-3.99740.16963480.14835742X-RAY DIFFRACTION95
3.9974-4.30590.15172940.13985880X-RAY DIFFRACTION95
4.3059-4.73910.14283280.12955788X-RAY DIFFRACTION95
4.7391-5.42450.1642650.1465185X-RAY DIFFRACTION84
5.4245-6.83270.19453040.16445925X-RAY DIFFRACTION96
6.8327-59.52050.18913230.19015646X-RAY DIFFRACTION90

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