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- PDB-1rdw: Actin Crystal Dynamics: Structural Implications for F-actin Nucle... -

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Basic information

Entry
Database: PDB / ID: 1rdw
TitleActin Crystal Dynamics: Structural Implications for F-actin Nucleation, Polymerization and Branching Mediated by the Anti-parallel Dimer
ComponentsActin, alpha skeletal muscle
KeywordsSTRUCTURAL PROTEIN / Anti-parallel dimer / Polymerization / Nucleation / Filament
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
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: 2.3 Å
AuthorsReutzel, R. / Yoshioka, C. / Govindasamy, L. / Yarmola, E.G. / Agbandje-Mckenna, M. / Bubb, M.R. / Mckenna, R.
CitationJournal: J.Struct.Biol. / Year: 2004
Title: Actin crystal dynamics: structural implications for F-actin nucleation, polymerization, and branching mediated by the anti-parallel dimer.
Authors: Reutzel, R. / Yoshioka, C. / Govindasamy, L. / Yarmola, E.G. / Agbandje-McKenna, M. / Bubb, M.R. / McKenna, R.
History
DepositionNov 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8405
Polymers41,8631
Non-polymers9774
Water2,036113
1
X: Actin, alpha skeletal muscle
hetero molecules

X: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,68010
Polymers83,7252
Non-polymers1,9558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)100.917, 100.917, 103.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11X-509-

HOH

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Components

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


Mass: 41862.613 Da / Num. of mol.: 1 / Fragment: ACtin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Tissue: muscleSkeletal muscle / Gene: ACTA1, ACTA / References: UniProt: P68135
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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-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 / Latrunculin


Mass: 421.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H31NO5S / Comment: toxin*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.7
Details: MgCl2, NH4SO4, pH 6.7, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / Details: Bubb, M.R., (2002) J. Biol. Chem., 277, 20999.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.3 Mammonium sulfate1reservoir
21.0 mMATP1reservoir
33.0 mM1reservoirMgCl2
460 mMimidazole1reservoirpH6.7

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: Osmic mirrors
RadiationMonochromator: CuKalpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 22951 / % possible obs: 93.9 % / Rsym value: 0.093
Reflection shellResolution: 2.3→2.38 Å / Num. unique all: 22951 / Rsym value: 0.424 / % possible all: 92.1
Reflection
*PLUS
Rmerge(I) obs: 0.093

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LCU

1lcu


Resolution: 2.3→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.224 -random
Rwork0.162 --
obs-22951 -
Displacement parametersBiso mean: 38.346 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 62 113 3004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.03
X-RAY DIFFRACTIONc_angle_d2.9
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.9

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