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- PDB-1lcu: Polylysine Induces an Antiparallel Actin Dimer that Nucleates Fil... -

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Basic information

Entry
Database: PDB / ID: 1lcu
TitlePolylysine Induces an Antiparallel Actin Dimer that Nucleates Filament Assembly: Crystal Structure at 3.5 A Resolution
ComponentsActin, alpha skeletal muscle
KeywordsCONTRACTILE PROTEIN / Structural protein / Muscle protein
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 / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / 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
Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / 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; Chain A, domain 2 / Actin; Chain A, domain 2 / 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 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBubb, M.R. / Govindasamy, L. / Yarmola, E.G. / Vorobiev, S.M. / Almo, S.C. / Somasundaram, T. / Chapman, M.S. / Agbandje-Mckenna, M. / Mckenna, R.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Polylysine induces an antiparallel actin dimer that nucleates filament assembly: crystal structure at 3.5-A resolution.
Authors: Bubb, M.R. / Govindasamy, L. / Yarmola, E.G. / Vorobiev, S.M. / Almo, S.C. / Somasundaram, T. / Chapman, M.S. / Agbandje-Mckenna, M. / Mckenna, R.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Effects of Jasplakinolide on the Kinetics of Actin Polymerization. AN EXPLANATION FOR CERTAIN IN VIVO OBSERVATIONS
Authors: Bubb, M.R. / Spector, I. / Beyer, B.B. / Fosen, K.M.
History
DepositionApr 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,81213
Polymers82,6882
Non-polymers2,12411
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-81 kcal/mol
Surface area31770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.456, 103.029, 126.958
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 , 1 types, 2 molecules AB

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


Mass: 41344.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135

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Non-polymers , 5 types, 95 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-LAR / LATRUNCULIN A / 4-(17-HYDROXY-5,12-DIMETHYL-3-OXO-2,16-DIOXABICYCLO[13.3.1]NONADECA-4,8,10-TRIEN-17-YL)-2-THIAZOLIDINONE


Mass: 421.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H31NO5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

CrystalDensity Matthews: 4.01 Å3/Da / Density % sol: 69.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, MgCl2, Imidazole, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / pH: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.240 mMactin1drop
20.120 mMpolylysine1drop
31.3 Mammonium sulfate1reservoir
41.0 mMATP1reservoir
53.0 mM1reservoirMgCl2
660 mMimidazole1reservoirpH6.7

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 4, 2000 / Details: OSMIC MIRROR
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 15407 / % possible obs: 88.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.115
Reflection shellHighest resolution: 3.5 Å / Rmerge(I) obs: 0.115 / Num. unique all: 15407 / % possible all: 88.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 101490
Reflection shell
*PLUS
Rmerge(I) obs: 0.249

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ESV

1esv


Resolution: 3.5→30 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Brunger & Adams
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 725 -random
Rwork0.1957 ---
obs-15407 88.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.067 Å2-3.376 Å20 Å2
2--0 Å21.309 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5725 0 127 84 5936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3955
LS refinement shellHighest resolution: 3.5 Å
RfactorNum. reflection% reflection
Rfree0.2661 725 -
Rwork0.1957 --
obs-15407 88.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2lar_cns.param
X-RAY DIFFRACTION3atp_cns.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5water_rep.param
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor all: 0.196 / Rfactor obs: 0.193 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.39

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