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- PDB-9l2n: Crystal structure of Cytochalasin D bound to a filamentous confor... -

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Basic information

Entry
Database: PDB / ID: 9l2n
TitleCrystal structure of Cytochalasin D bound to a filamentous conformation actin
Components
  • Actin, alpha skeletal muscle
  • Actin-binding protein fragmin P
KeywordsCYTOSOLIC PROTEIN / Actin dynamics / Cytochalasin / Actin drugs
Function / homology
Function and homology information


Striated Muscle Contraction / actin polymerization or depolymerization / striated muscle thin filament / skeletal muscle thin filament assembly / stress fiber / skeletal muscle fiber development / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton ...Striated Muscle Contraction / actin polymerization or depolymerization / striated muscle thin filament / skeletal muscle thin filament assembly / stress fiber / skeletal muscle fiber development / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton / hydrolase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. ...Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain 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'-DIPHOSPHATE / Chem-CY9 / PHOSPHATE ION / Actin, alpha skeletal muscle / Actin-binding protein fragmin P
Similarity search - Component
Biological speciesPhysarum polycephalum (eukaryote)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTakeda, S. / Maeda, Y. / Fujiwara, I.
Funding support Japan, 5items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K17708 Japan
Japan Society for the Promotion of Science (JSPS)17K07373 Japan
Japan Society for the Promotion of Science (JSPS)20K06522 Japan
Japan Society for the Promotion of Science (JSPS)22K06172 Japan
Japan Society for the Promotion of Science (JSPS)23K05666 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Microscopic and structural observations of actin filament capping and severing by cytochalasin D
Authors: Mitani, T. / Takeda, S. / Oda, T. / Narita, A. / Maeda, Y. / Honda, H. / Fujiwara, I.
History
DepositionDec 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,53412
Polymers60,0862
Non-polymers1,44810
Water15,367853
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-61 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.213, 90.806, 114.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139
#2: Protein Actin-binding protein fragmin P


Mass: 18210.404 Da / Num. of mol.: 1 / Mutation: N13A
Source method: isolated from a genetically manipulated source
Details: The first two residues (GP) were derived from the expression tag. Asn13 in the original sequence (Asn15 due to the addition of the first two residues) was replaced with Ala.
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94707

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Non-polymers , 7 types, 863 molecules

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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CY9 / (3S,3aR,4S,6S,6aR,7E,10S,12R,13E,15R,15aR)-3-benzyl-6,12-dihydroxy-4,10,12-trimethyl-5-methylidene-1,11-dioxo-2,3,3a,4,5,6,6a,9,10,11,12,15-dodecahydro-1H-cycloundeca[d]isoindol-15-yl acetate / Cytochalasin D


Mass: 507.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H37NO6 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor, alkaloid, toxin*YM
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 853 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 17% (w/v) PEG3350 and 20 mM Na2HPO4

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.7→48.45 Å / Num. obs: 65908 / % possible obs: 99.5 % / Redundancy: 4.73 % / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.141 / Net I/σ(I): 8.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.84.720.9024.72104660.6321.01598.9
1.8-1.934.780.5734.7899130.8260.64499.9
1.93-2.080.3374.892750.9170.37999.9
2.08-2.280.2294.885860.9620.25899.9
2.28-2.550.1644.7777400.9790.18499.8
2.55-2.940.1184.7268950.9880.13399.8
2.94-3.60.0774.5958420.9940.08799.3
3.6-5.080.0514.5845520.9960.05798.5
5.08-48.4450.0424.5826380.9980.04897.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7w50

7w50


Resolution: 1.7→42.21 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2045 3295 5 %
Rwork0.1747 --
obs0.1762 65902 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 90 853 4815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114176
X-RAY DIFFRACTIONf_angle_d0.965695
X-RAY DIFFRACTIONf_dihedral_angle_d15.9211535
X-RAY DIFFRACTIONf_chiral_restr0.06622
X-RAY DIFFRACTIONf_plane_restr0.008729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.3281300.28552471X-RAY DIFFRACTION96
1.73-1.750.26181370.25752591X-RAY DIFFRACTION100
1.75-1.780.26011360.23472600X-RAY DIFFRACTION100
1.78-1.810.27031350.2242560X-RAY DIFFRACTION100
1.81-1.840.2571360.21942587X-RAY DIFFRACTION100
1.84-1.870.25011370.22762602X-RAY DIFFRACTION100
1.87-1.910.24571370.22212591X-RAY DIFFRACTION100
1.91-1.950.30611370.23192602X-RAY DIFFRACTION100
1.95-1.990.23121350.1952566X-RAY DIFFRACTION100
1.99-2.040.2091380.18152618X-RAY DIFFRACTION100
2.04-2.090.19831360.17622593X-RAY DIFFRACTION100
2.09-2.140.20791370.17342601X-RAY DIFFRACTION100
2.14-2.210.22931370.17392613X-RAY DIFFRACTION100
2.21-2.280.21521380.1982607X-RAY DIFFRACTION100
2.28-2.360.22081360.17082587X-RAY DIFFRACTION100
2.36-2.450.19031380.17392618X-RAY DIFFRACTION100
2.45-2.570.23021370.1722619X-RAY DIFFRACTION100
2.57-2.70.23131380.17142608X-RAY DIFFRACTION100
2.7-2.870.23861390.17152642X-RAY DIFFRACTION100
2.87-3.090.19141380.16842624X-RAY DIFFRACTION100
3.09-3.40.20171380.16182635X-RAY DIFFRACTION99
3.4-3.890.16921400.14512641X-RAY DIFFRACTION99
3.89-4.90.15021400.1292671X-RAY DIFFRACTION99
4.91-42.210.15791450.17222760X-RAY DIFFRACTION98

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