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- PDB-8c47: Leishmania ATP-actin monomer in complex with Leishmania profilin -

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Basic information

Entry
Database: PDB / ID: 8c47
TitleLeishmania ATP-actin monomer in complex with Leishmania profilin
Components
  • Actin
  • Profilin
KeywordsSTRUCTURAL PROTEIN / Actin / profilin / leishmania / cytoskeleton
Function / homology
Function and homology information


kinetoplast / sequestering of actin monomers / actin monomer binding / cell cortex / endonuclease activity / cytoskeleton / chromatin remodeling / ATP binding
Similarity search - Function
Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. ...Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Profilin / Actin
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKogan, K. / Kotila, T.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland302161 Finland
Jane and Aatos Erkko Foundation4708679 Finland
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Leishmania profilin interacts with actin through an unusual structural mechanism to control cytoskeletal dynamics in parasites.
Authors: Vizcaino-Castillo, A. / Kotila, T. / Kogan, K. / Yanase, R. / Como, J. / Antenucci, L. / Michelot, A. / Sunter, J.D. / Lappalainen, P.
History
DepositionJan 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Profilin
A: Actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8496
Polymers58,1182
Non-polymers7314
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-33 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.297, 171.297, 43.694
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Components on special symmetry positions
IDModelComponents
11A-660-

HOH

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Components

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Protein , 2 types, 2 molecules BA

#1: Protein Profilin


Mass: 16185.040 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_32_0520 / Plasmid: pPL1718 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4Q5N1
#2: Protein Actin


Mass: 41932.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: ACT, LMJF_04_1230 / Plasmid: pPL1698 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9U1E8

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Non-polymers , 4 types, 247 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, PEG4000 26% (w/v) and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→33.59 Å / Num. obs: 32700 / % possible obs: 99.83 % / Redundancy: 7.7 % / Biso Wilson estimate: 49.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.034 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 1.234 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2799 / CC1/2: 0.799 / Rpim(I) all: 0.472 / % possible all: 99.72

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSBUILT 20191211data reduction
Aimless0.7.2data scaling
MOLREPArpWarp web server V8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.16 Å / SU ML: 0.2519 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 1668 5.11 %RANDOM
Rwork0.1932 30988 --
obs0.1949 32656 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3949 0 44 243 4236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224103
X-RAY DIFFRACTIONf_angle_d0.48855567
X-RAY DIFFRACTIONf_chiral_restr0.046606
X-RAY DIFFRACTIONf_plane_restr0.004717
X-RAY DIFFRACTIONf_dihedral_angle_d5.8319558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.32891350.28312560X-RAY DIFFRACTION99.74
2.26-2.340.30391370.26082537X-RAY DIFFRACTION99.85
2.34-2.420.3351600.27992536X-RAY DIFFRACTION99.67
2.42-2.520.32581380.25362546X-RAY DIFFRACTION99.85
2.52-2.630.31581150.24612607X-RAY DIFFRACTION99.96
2.63-2.770.28571540.23562532X-RAY DIFFRACTION99.89
2.77-2.950.26291390.24512575X-RAY DIFFRACTION99.96
2.95-3.170.25931350.21782576X-RAY DIFFRACTION99.96
3.17-3.490.22781270.20572598X-RAY DIFFRACTION100
3.49-3.990.20711450.16822603X-RAY DIFFRACTION100
4-5.030.17361700.15112586X-RAY DIFFRACTION100
5.03-32.160.19641130.16682732X-RAY DIFFRACTION99.89
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)
13.81595168894-0.314589988584-0.6515574388824.16829402510.7837065564512.97588997390.096921055714-0.163486901970.2321307510930.4155065163520.0166465400116-0.0620582624765-0.334958223997-0.0638513135787-0.1063736211030.4210038698780.05904743215320.03622298420820.3019012991840.05843001210270.281830851637-4.2933442003224.30479807087.14626290162
24.17458432135-1.17450908695-0.2279482286081.814753263720.05594030355621.34836536832-0.15769647628-0.1952249997150.1022219817990.2430123419710.23197736827-0.296518371515-0.126580563680.297505166188-0.08704134752790.323101204334-0.0287916235151-0.02100625696510.396819655004-0.003747754203170.30435146428323.70812744728.01117078986-3.11551649348
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 2 through 150)BA2 - 1503 - 151
22(chain 'A' and resid 6 through 375)AC6 - 3751 - 358

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