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- PDB-3eku: Crystal Structure of Monomeric Actin bound to Cytochalasin D -

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Basic information

Entry
Database: PDB / ID: 3eku
TitleCrystal Structure of Monomeric Actin bound to Cytochalasin D
ComponentsActin-5C
KeywordsCONTRACTILE PROTEIN / Motor protein / ATP-state / fungal toxin / Acetylation / ATP-binding / Cytoplasm / Cytoskeleton / Nucleotide-binding
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Recycling pathway of L1 / VEGFA-VEGFR2 Pathway / : / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle ...Gap junction degradation / Formation of annular gap junctions / EPHB-mediated forward signaling / EPH-ephrin mediated repulsion of cells / Recycling pathway of L1 / VEGFA-VEGFR2 Pathway / : / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / RHOF GTPase cycle / MAP2K and MAPK activation / Platelet degranulation / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / DNA Damage Recognition in GG-NER / UCH proteinases / Clathrin-mediated endocytosis / sperm individualization / brahma complex / maintenance of protein location in cell / tube formation / Ino80 complex / mitotic cytokinesis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoskeleton / hydrolase activity / chromatin remodeling / ATP binding / cytoplasm
Similarity search - Function
ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family ...ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / 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 / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-CY9 / Actin-5C
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsNair, U.B. / Joel, P.B. / Wan, Q. / Lowey, S. / Rould, M.A. / Trybus, K.M.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of monomeric actin bound to cytochalasin D.
Authors: Nair, U.B. / Joel, P.B. / Wan, Q. / Lowey, S. / Rould, M.A. / Trybus, K.M.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Crystal Structures of Expressed Non-polymerizable Monomeric Actin in the ADP and ATP states
Authors: Rould, M.A. / Wan, Q. / Joel, P.B. / Lowey, S. / Trybus, K.M.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin-5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9225
Polymers41,8271
Non-polymers1,0954
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)207.400, 54.040, 36.890
Angle α, β, γ (deg.)90.000, 98.960, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Actin-5C


Mass: 41826.668 Da / Num. of mol.: 1 / Mutation: A204E, P243K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Act5C, CG4027 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P10987
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: 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 / Cytochalasin D


Mass: 507.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H37NO6 / Comment: inhibitor, alkaloid, toxin*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4449.61
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop5.220% MPD, 0.1M sodium acetate, 0.1M NaCl, 0.02M CaCl2, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop5.220% MPD, 0.1M sodium acetate, 0.1M NaCl, 0.02M CaCl2, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU RUH3R11.5418
ROTATING ANODERIGAKU RUH3R21.5418
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATESep 9, 2003
MAR scanner 345 mm plate2IMAGE PLATESep 16, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1XENOCS MULTILAYER OPTICSSINGLE WAVELENGTHMx-ray1
2XENOCS MULTILAYER OPTICSSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 13808 / Num. obs: 13808 / % possible obs: 97.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.108 / Χ2: 1.161 / Net I/σ(I): 16.1
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1190 / Χ2: 0.74 / % possible all: 85.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
EPMRphasing
RefinementStarting model: PDB ENTRY 2HF4

2hf4


Resolution: 2.5→15 Å / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1313 9.3 %random
Rwork0.177 ---
all0.201 13323 --
obs0.201 13323 94.5 %-
Solvent computationBsol: 36.495 Å2
Displacement parametersBiso max: 70.41 Å2 / Biso mean: 27.25 Å2 / Biso min: 1.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.918 Å20 Å2-0.891 Å2
2--5.939 Å20 Å2
3----7.856 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 0 70 249 3139
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2721.5
X-RAY DIFFRACTIONc_scbond_it1.9542
X-RAY DIFFRACTIONc_mcangle_it2.0772
X-RAY DIFFRACTIONc_scangle_it2.8562.5
X-RAY DIFFRACTIONc_bond_d0.0059
X-RAY DIFFRACTIONc_angle_deg1.22
LS refinement shellResolution: 2.5→2.53 Å
RfactorNum. reflection
Rfree0.2439 39
Rwork0.2285 -
obs-366
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2cns_atp_param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5cytD_prodrg_012607_nomin.par

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