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- PDB-8j64: Crystal structure of Toxoplasma gondii MIC2-M2AP complex -

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Basic information

Entry
Database: PDB / ID: 8j64
TitleCrystal structure of Toxoplasma gondii MIC2-M2AP complex
Components
  • MIC2-associated protein
  • Micronemal protein MIC2
KeywordsCELL INVASION / Toxoplasma gondii / MIC2 / M2AP / TSR6 domain / structural biology
Function / homology
Function and homology information


Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Micronemal protein MIC2 / MIC2-associated protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, S. / Wang, F.F. / Zhang, D.J. / Song, G.J. / Springer, T.A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171215 China
CitationJournal: Commun Biol / Year: 2023
Title: Structural insights into MIC2 recognition by MIC2-associated protein in Toxoplasma gondii.
Authors: Zhang, S. / Wang, F. / Zhang, D. / Liu, D. / Ding, W. / Springer, T.A. / Song, G.
History
DepositionApr 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MIC2-associated protein
B: Micronemal protein MIC2


Theoretical massNumber of molelcules
Total (without water)26,1132
Polymers26,1132
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-9 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.777, 53.176, 95.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MIC2-associated protein / MIC2-associated protein M2AP


Mass: 19685.992 Da / Num. of mol.: 1 / Mutation: N127R, S177N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_039670 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: Q967S9
#2: Protein Micronemal protein MIC2 / Microneme protein MIC2


Mass: 6427.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_037170 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: O00816
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% glycerol, 0.2M sodium acetate trihydrate, 0.1M TRIS hydrochloride pH 8.5, 30% w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→23.03 Å / Num. obs: 14640 / % possible obs: 95.6 % / Redundancy: 8.8 % / Biso Wilson estimate: 12.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Χ2: 0.99 / Net I/σ(I): 27.2
Reflection shellResolution: 2→2.15 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 16.2 / Num. unique obs: 838 / CC1/2: 0.993 / Χ2: 0.92 / % possible all: 76.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootv1.0model building
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→23.03 Å / SU ML: 0.141 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.3216
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2114 767 5.25 %
Rwork0.1752 13836 -
obs0.177 14603 95.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.86 Å2
Refinement stepCycle: LAST / Resolution: 2→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 0 270 1943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021707
X-RAY DIFFRACTIONf_angle_d0.51912315
X-RAY DIFFRACTIONf_chiral_restr0.0449261
X-RAY DIFFRACTIONf_plane_restr0.0045299
X-RAY DIFFRACTIONf_dihedral_angle_d5.2785229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.19841320.16642406X-RAY DIFFRACTION84.52
2.15-2.370.19241440.18062862X-RAY DIFFRACTION99.83
2.37-2.710.24021440.19522884X-RAY DIFFRACTION99.9
2.71-3.420.2191820.17812877X-RAY DIFFRACTION99.9
3.42-23.030.20551650.16342807X-RAY DIFFRACTION92.59
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44943570646-0.5327603227160.543013215480.7483636412-0.2837167396520.9885763016630.04146403671320.00814797555121-0.169203436622-0.01556566557740.01021329447320.07456177898050.116458306269-0.0375837478155-0.02763937141970.0516795364185-0.01310197013440.007710824901480.0476116710463-0.000826659941310.05834183865797.087688593694.8377885768114.1267369617
21.93939339251-0.3278150081360.6313765562832.22572763561-0.1949668233461.5143028241-0.0299834295736-0.12179512635-0.1034564250970.3272597007530.03766724344140.0313540280464-0.02564966989630.0215100318658-0.007131022335870.0971783297099-0.006659119091530.01570775247060.0432839271518-0.02003832850190.055610629572617.457482116614.721190181923.844249717
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A'AA44 - 2281 - 173
22chain 'B'BB596 - 6441 - 49

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