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- PDB-6w7v: Structure of rabbit actin in complex with truncated analog of Myc... -

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Basic information

Entry
Database: PDB / ID: 6w7v
TitleStructure of rabbit actin in complex with truncated analog of Mycalolide B
ComponentsActin, alpha skeletal muscle
KeywordsCONTRACTILE PROTEIN / actin / toxin / complex
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
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 / LATRUNCULIN B / Chem-TFJ / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAllingham, J.S. / Deng, X. / Trofimova, D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)151976 Canada
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Truncated Actin-Targeting Macrolide Derivative Blocks Cancer Cell Motility and Invasion of Extracellular Matrix.
Authors: Pipaliya, B.V. / Trofimova, D.N. / Grange, R.L. / Aeluri, M. / Deng, X. / Shah, K. / Craig, A.W. / Allingham, J.S. / Evans, P.A.
History
DepositionMar 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8258
Polymers42,0971
Non-polymers1,7287
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Actin polymerizes in the presence of polymerizing buffer. This actin polymerization is severely inhibited in the presence of the ligand (synthetic toxin).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-12 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.763, 74.869, 61.197
Angle α, β, γ (deg.)90.000, 93.023, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 42096.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: heart / References: UniProt: P68135

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Non-polymers , 6 types, 318 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Chemical ChemComp-LAB / LATRUNCULIN B / Latrunculin


Mass: 395.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO5S / Comment: toxin*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TFJ / (1E,3R,4R,5S,6R,9S,10S,12S)-12-[(4-aminobutanoyl)oxy]-1-[ethyl(formyl)amino]-4,10-dimethoxy-3,5,9,13-tetramethyltetradec-1-en-6-yl (2R)-oxolane-2-carboxylate


Mass: 598.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O8 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl, pH 8.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.7→37.71 Å / Num. obs: 43140 / % possible obs: 97.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.76 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.4
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 3601 / CC1/2: 0.998 / % possible all: 97.38

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MGO

6mgo


Resolution: 1.7→37.71 Å / SU ML: 0.3546 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2127 1827 4.95 %
Rwork0.179 35061 -
obs0.1808 36888 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.07 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 113 311 3225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142975
X-RAY DIFFRACTIONf_angle_d1.43894035
X-RAY DIFFRACTIONf_chiral_restr0.0621452
X-RAY DIFFRACTIONf_plane_restr0.0091508
X-RAY DIFFRACTIONf_dihedral_angle_d18.8956431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.61391300.62622658X-RAY DIFFRACTION97.31
1.75-1.80.46951460.4522658X-RAY DIFFRACTION97.19
1.8-1.860.35791300.31922679X-RAY DIFFRACTION98.32
1.86-1.920.30911410.23612649X-RAY DIFFRACTION97.83
1.92-20.2781220.21462693X-RAY DIFFRACTION97.57
2-2.090.2441340.19652681X-RAY DIFFRACTION98.22
2.09-2.20.23071290.19252701X-RAY DIFFRACTION98.5
2.2-2.340.21651410.16542704X-RAY DIFFRACTION98.75
2.34-2.520.20191570.15742692X-RAY DIFFRACTION98.96
2.52-2.770.21331410.15782714X-RAY DIFFRACTION99.2
2.77-3.170.17251570.15522705X-RAY DIFFRACTION99.38
3.17-3.990.1781670.13912715X-RAY DIFFRACTION99.45
4-37.710.15471320.14592812X-RAY DIFFRACTION99.76

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