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- PDB-36oq: Structure of rabbit actin bound to a truncated Mycalolide B analo... -

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Basic information

Entry
Database: PDB / ID: 36oq
TitleStructure of rabbit actin bound to a truncated Mycalolide B analogue containing an expanded cyclohexane moiety
ComponentsActin, alpha skeletal muscle
KeywordsCONTRACTILE PROTEIN / Actin monomer / Cytoskeleton / Actin-small molecule complex / antimetastatic agent
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / skeletal muscle myofibril / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / skeletal muscle myofibril / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / actin filament polymerization / stress fiber / titin binding / 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 / protein domain specific binding / positive regulation of gene expression / calcium ion binding / magnesium ion binding / ATP hydrolysis activity / 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 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsAlexander, C.K. / Trofimova, D. / Allingham, J.S.
Funding support Canada, 5items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)134763 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)151976 Canada
Other governmentNFRFE-2019-01485 Canada
Other private Canada
Other private Canada
CitationJournal: To Be Published
Title: Actin-binding is not enough: solvent-facing substituents maximize cellular efficacy of actin-disrupting macrolide analogues
Authors: Trofimova, D. / Alexander, C.K. / Jiang, Y. / Veeranna, K.D. / Craig, A.W. / Evans, A.P. / Allingham, J.S.
History
DepositionJun 24, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8716
Polymers41,2271
Non-polymers1,6445
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.850, 75.310, 61.950
Angle α, β, γ (deg.)90.00, 92.44, 90.00
Int Tables number4
Space group name H-MP1211

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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: 41227.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Non-polymers , 6 types, 205 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO5S / Comment: toxin*YM
#6: Chemical ChemComp-A1DK1 / (3R,4R,5S,6R,9S,10S,12S,E)-12-((4-aminobutanoyl)oxy)-12-cyclohexyl-1-(N-ethylformamido)-4,10-dimethoxy-3,5,9-trimethyldodec-1-en-6-yl (R)-tetrahydrofuran-2-carboxylate


Mass: 638.875 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H62N2O8 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 200 mM MgCl2 , 100 mM TRIS-HCl pH 6.5
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95371 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 5, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 1.72→47.86 Å / Num. obs: 36870 / % possible obs: 99.9 % / Redundancy: 6.85 % / Biso Wilson estimate: 33.494 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.133 / Rrim(I) all: 0.144 / Net I/σ(I): 8.3
Reflection shellResolution: 1.72→1.77 Å / Mean I/σ(I) obs: 1.47 / Num. unique obs: 2987 / CC1/2: 0.704 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→47.86 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.949 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22933 2012 5.5 %RANDOM
Rwork0.17899 ---
obs0.1817 34858 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å2-0 Å21.81 Å2
2---1.69 Å20 Å2
3---3.16 Å2
Refinement stepCycle: 1 / Resolution: 1.72→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2818 0 108 200 3126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123043
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162872
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.8414138
X-RAY DIFFRACTIONr_angle_other_deg0.551.7826644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0095372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.942525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98610511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4242.9961461
X-RAY DIFFRACTIONr_mcbond_other2.4242.9981462
X-RAY DIFFRACTIONr_mcangle_it3.3175.3671830
X-RAY DIFFRACTIONr_mcangle_other3.3175.3691831
X-RAY DIFFRACTIONr_scbond_it3.4893.4621582
X-RAY DIFFRACTIONr_scbond_other3.4883.4621583
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4026.1562305
X-RAY DIFFRACTIONr_long_range_B_refined7.02230.143411
X-RAY DIFFRACTIONr_long_range_B_other6.99529.653364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 150 -
Rwork0.325 2533 -
obs--99.67 %

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