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- PDB-4gft: Malaria invasion machinery protein-Nanobody complex -

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Basic information

Entry
Database: PDB / ID: 4gft
TitleMalaria invasion machinery protein-Nanobody complex
Components
  • Myosin A tail domain interacting protein
  • NanobodySingle-domain antibody
Keywordsprotein binding / immune system / Malaria invasion machinery protein / MTIP / MYOA TAIL INTERACTING PROTEIN / NANOBODY
Function / homology
Function and homology information


glideosome / inner membrane pellicle complex / myosin II complex / calcium ion binding
Similarity search - Function
: / Myosin A tail domain interacting protein, N-terminal / EF-hand domain / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulins / Immunoglobulin-like ...: / Myosin A tail domain interacting protein, N-terminal / EF-hand domain / EF-hand / Recoverin; domain 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Myosin A tail domain interacting protein
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKhamrui, S. / Turley, S. / Pardon, E. / Steyaert, J. / Verlinde, C. / Fan, E. / Bergman, L.W. / Hol, W.G.J.
CitationJournal: Mol.Biochem.Parasitol. / Year: 2013
Title: The structure of the D3 domain of Plasmodium falciparum myosin tail interacting protein MTIP in complex with a nanobody.
Authors: Khamrui, S. / Turley, S. / Pardon, E. / Steyaert, J. / Fan, E. / Verlinde, C.L. / Bergman, L.W. / Hol, W.G.
History
DepositionAug 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Other
Revision 1.2Dec 9, 2015Group: Database references
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin A tail domain interacting protein
B: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7174
Polymers22,5932
Non-polymers1242
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint0 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.848, 52.951, 73.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myosin A tail domain interacting protein


Mass: 7856.606 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (unp residues 137-204) / Mutation: C155S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: MTIP, PFL2225w / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta / References: UniProt: Q8I4W8
#2: Antibody Nanobody / Single-domain antibody


Mass: 14736.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 25% PEG3350, 50 mM ammonium sulfate, 0.1 M TrisHCl, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→35.6 Å / Num. all: 152128 / Num. obs: 23569 / % possible obs: 94.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.8 / % possible all: 87.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→35.53 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.443 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20466 1261 5.1 %RANDOM
Rwork0.18121 ---
obs0.18239 23568 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.056 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å2-0 Å2
2---0.81 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 8 108 1556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021483
X-RAY DIFFRACTIONr_bond_other_d0.0010.021342
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9362009
X-RAY DIFFRACTIONr_angle_other_deg0.8413.0013069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.87824.55968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70615227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.751157
X-RAY DIFFRACTIONr_chiral_restr0.120.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021738
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 93 -
Rwork0.339 1586 -
obs--91.8 %
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)
117.895125.5397-12.792572.768-11.41914.4969-2.69892.0771-1.0044-2.77251.76751.02693.4054-2.31430.93141.345-0.73060.16760.6386-0.14080.24339.812-11.077-38.678
23.0570.1034-4.66443.9667-1.59788.6707-0.21690.0681-0.0539-0.28780.0697-0.00970.517-0.16950.14720.098-0.01240.03650.08360.0190.035115.349-1.027-39.13
366.25454.20161.389532.387416.982963.10040.85580.39760.4604-1.6865-0.46874.0740.6773-0.8778-0.3870.2031-0.0456-0.2640.2430.03950.69776.072-0.929-35.171
455.078249.3187-10.108450.09126.724643.8325-1.5020.7941-1.174-0.4057-0.1917-0.50612.7827-2.49061.69370.4623-0.21780.08550.74430.08610.89932.023-7.462-35.619
55.04111.7799.425333.92991.739923.00470.3974-0.0479-0.1715-0.9698-0.24870.41281.1037-0.1378-0.14870.12130.007-0.00750.07690.00030.04950.458-2.653-27.219
67.13771.366-0.52092.30350.24.3455-0.0926-0.1158-0.0396-0.0720.1019-0.1575-0.07870.2903-0.00930.04930.02720.01230.0810.0230.035810.056-1.42-24.82
716.7116-5.3034-12.192312.88726.374926.12190.1013-0.73170.87040.6528-0.0294-0.3377-0.71080.8818-0.0720.1418-0.009-0.03430.127-0.00350.103317.7992.796-30.059
86.63363.6708-8.26299.9107-7.035714.8256-0.41360.0061-0.2736-0.4264-0.0097-0.31280.84060.17350.42330.17570.0480.05470.1040.00250.103915.164-9.708-30.41
91.3213-0.19452.3242.1961-3.741916.0393-0.0468-0.11270.00740.18280.06980.0978-0.1472-0.1548-0.0230.08210.00190.00960.063-0.00250.02681.937-8.193-6.945
1023.64435.296612.20833.87316.224915.86670.6395-0.3466-0.11020.1699-0.3614-0.18570.8190.0048-0.27810.2351-0.022-0.07770.13490.06840.07719.27-21.5387.246
111.5938-0.30240.42831.4548-0.3761.65870.0035-0.03780.06630.06050.01340.0332-0.0321-0.0279-0.01690.0381-0.0065-0.02260.0421-0.00410.02414.155-12.521-12.124
1260.809721.47241.905224.319124.309634.2851-0.52750.16760.8913-0.77530.2572-0.2954-0.69690.23830.27030.2318-0.08820.01220.21240.02480.076918.613-9.82-7.919
138.43011.76695.01193.00750.75485.0110.18470.3484-0.4003-0.22030.0665-0.19430.21850.334-0.25120.06190.0163-0.01890.0607-0.02690.03887.819-22.716-15.28
143.8958-1.08292.50123.4881-0.31044.06020.0054-0.0833-0.15640.27750.0758-0.06170.1401-0.0141-0.08120.0601-0.0062-0.0130.05090.00660.02244.552-21.563-7.341
150.3697-0.36610.74721.713-0.76714.04370.02720.048-0.00780.0102-0.0373-0.28650.06640.23850.01010.0402-0.0094-0.01540.09630.00130.080410.894-13.177-12.869
169.3612-12.488614.413221.5465-24.832228.6194-0.3103-0.5467-0.07530.63830.2952-0.0107-0.7379-0.34580.01520.1556-0.0124-0.0510.12350.00260.043610.365-11.7814.057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A140 - 148
2X-RAY DIFFRACTION2A149 - 164
3X-RAY DIFFRACTION3A165 - 168
4X-RAY DIFFRACTION4A169 - 174
5X-RAY DIFFRACTION5A175 - 178
6X-RAY DIFFRACTION6A179 - 189
7X-RAY DIFFRACTION7A190 - 193
8X-RAY DIFFRACTION8A194 - 204
9X-RAY DIFFRACTION9B2 - 12
10X-RAY DIFFRACTION10B13 - 19
11X-RAY DIFFRACTION11B20 - 44
12X-RAY DIFFRACTION12B45 - 48
13X-RAY DIFFRACTION13B49 - 64
14X-RAY DIFFRACTION14B65 - 87
15X-RAY DIFFRACTION15B88 - 117
16X-RAY DIFFRACTION16B118 - 127

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