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- PDB-4lv8: Murine IRGa6 bound to Toxoplasma ROP5C, a pseudokinase GDI -

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Basic information

Entry
Database: PDB / ID: 4lv8
TitleMurine IRGa6 bound to Toxoplasma ROP5C, a pseudokinase GDI
Components
  • Interferon-inducible GTPase 1
  • Rhoptry protein 5 C
KeywordsTransferase/Hydrolase / immune related GTPase / guanine dissociation inhibitor / parasite effector / Transferase-Hydrolase complex
Function / homology
Function and homology information


symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / cellular response to interferon-beta / regulation of autophagy / response to bacterium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response / cytokine-mediated signaling pathway / GDP binding ...symbiont-containing vacuole membrane / Golgi cisterna membrane / defense response to protozoan / cellular response to interferon-beta / regulation of autophagy / response to bacterium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response / cytokine-mediated signaling pathway / GDP binding / nuclear membrane / defense response to Gram-negative bacterium / protein kinase activity / innate immune response / GTPase activity / GTP binding / endoplasmic reticulum membrane / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Rhoptry protein, Rop2-like / Protein kinase-like domain, Apicomplexa / Kinase-like / Immunity-related GTPases-like / IRG-type guanine nucleotide-binding (G) domain / Interferon-inducible GTPase (IIGP) / IRG-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...Rhoptry protein, Rop2-like / Protein kinase-like domain, Apicomplexa / Kinase-like / Immunity-related GTPases-like / IRG-type guanine nucleotide-binding (G) domain / Interferon-inducible GTPase (IIGP) / IRG-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / Rhoptry protein 5 C / Interferon-inducible GTPase 1
Similarity search - Component
Biological speciesToxoplasma gondii type I (eukaryote)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsReese, M.L. / Boothroyd, J.C.
CitationJournal: To be Published
Title: Murine IRGa6 bound to Toxoplasma ROP5C, a pseudokinase GDI
Authors: Reese, M.L. / Shah, N. / Boothroyd, J.C.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Derived calculations
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhoptry protein 5 C
B: Interferon-inducible GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,34715
Polymers89,8322
Non-polymers1,51513
Water9,278515
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Rhoptry protein 5 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1098
Polymers41,3471
Non-polymers7627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Interferon-inducible GTPase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2387
Polymers48,4841
Non-polymers7546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.400, 53.700, 86.800
Angle α, β, γ (deg.)104.700, 95.300, 111.000
Int Tables number1
Space group name H-MP1
Detailsbiological unit is the same as asym.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Rhoptry protein 5 C /


Mass: 41347.324 Da / Num. of mol.: 1 / Fragment: UNP residues 175-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii type I (eukaryote) / Strain: RH / Gene: ROP5C / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6ZQR7
#2: Protein Interferon-inducible GTPase 1 /


Mass: 48484.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Iigp1, Irga6 / Plasmid: pGEX4T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9QZ85, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement

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Non-polymers , 5 types, 528 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% PEG 20,000, 0.1M MES 5.8, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.72→38.669 Å / Num. obs: 90541 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 35.36 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.43
Reflection shell

Rmerge(I) obs: 0.02 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.72-1.761.52917676698100
1.76-1.811.8987038653099.8
1.81-1.872.4688007636399.9
1.87-1.923.1786290618899.9
1.92-1.994.3182848599399.9
1.99-2.065.2475963577099.9
2.06-2.137.08764385562100
2.13-2.229.3872737538899.9
2.22-2.3211.8373276513799.9
2.32-2.4314.3669903493499.8
2.43-2.5617.665131468399.9
2.56-2.7221.7758858441299.9
2.72-2.9128.31573204142100
2.91-3.1436.6656984390299.8
3.14-3.4447.7450849353099.9
3.44-3.8558.9543415323999.7
3.85-4.4471.6839090283199.9
4.44-5.4478.6835191240099.7
5.44-7.6971.8424847184199.4
7.69101.581493599899

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
XSCALEdata scaling
PDB_EXTRACT3.11data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q60 and then 1TPZ:A using phaser

3q60

1tpz


Resolution: 1.72→38.669 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.21 / σ(F): 1.97 / Phase error: 28.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1361 1.5 %
Rwork0.1951 --
obs0.1957 90512 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.43 Å2 / Biso mean: 35.9118 Å2 / Biso min: 13.34 Å2
Refinement stepCycle: LAST / Resolution: 1.72→38.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5991 0 96 515 6602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076293
X-RAY DIFFRACTIONf_angle_d1.1288523
X-RAY DIFFRACTIONf_chiral_restr0.079964
X-RAY DIFFRACTIONf_plane_restr0.0051086
X-RAY DIFFRACTIONf_dihedral_angle_d14.4352387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.72-1.78150.37511330.342489559088
1.7815-1.85280.34011430.30388779020
1.8528-1.93720.32431380.26388939031
1.9372-2.03930.26791300.234889109040
2.0393-2.1670.26261310.208989679098
2.167-2.33430.22671430.196889079050
2.3343-2.56920.26261360.195688969032
2.5692-2.94090.24031340.194889159049
2.9409-3.70470.2131360.18488959031
3.7047-38.67840.18721370.164689369073

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