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- PDB-3daw: Structure of the actin-depolymerizing factor homology domain in c... -

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Basic information

Entry
Database: PDB / ID: 3daw
TitleStructure of the actin-depolymerizing factor homology domain in complex with actin
Components
  • Actin, alpha skeletal muscle
  • Twinfilin-1
KeywordsSTRUCTURAL PROTEIN/STRUCTURAL PROTEIN REGULATOR / ACTIN DEPOLYMERISATION / ACTIN BINDING PROTEINS / CYTOSKELETON / STRUCTURAL PROTEIN-CONTRACTILE PROTEIN COMPLEX / STRUCTURAL PROTEIN-STRUCTURAL PROTEIN REGULATOR COMPLEX
Function / homology
Function and homology information


regulation of actin phosphorylation / RHOBTB2 GTPase cycle / sequestering of actin monomers / negative regulation of actin filament polymerization / barbed-end actin filament capping / actin filament depolymerization / regulation of lamellipodium assembly / cytoskeletal motor activator activity / tropomyosin binding / myofibril ...regulation of actin phosphorylation / RHOBTB2 GTPase cycle / sequestering of actin monomers / negative regulation of actin filament polymerization / barbed-end actin filament capping / actin filament depolymerization / regulation of lamellipodium assembly / cytoskeletal motor activator activity / tropomyosin binding / myofibril / myosin heavy chain binding / mesenchyme migration / troponin I binding / positive regulation of cardiac muscle hypertrophy / 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 / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / positive regulation of neuron projection development / calcium-dependent protein binding / actin filament binding / cell-cell junction / actin cytoskeleton / lamellipodium / cell body / actin binding / protein tyrosine kinase activity / hydrolase activity / protein domain specific binding / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Twinfilin / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily ...Twinfilin / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 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 / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle / Twinfilin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPaavilainen, V.O. / Oksanen, E. / Goldman, A. / Lappalainen, P.
CitationJournal: J.Cell Biol. / Year: 2008
Title: Structure of the actin-depolymerizing factor homology domain in complex with actin
Authors: Paavilainen, V.O. / Oksanen, E. / Goldman, A. / Lappalainen, P.
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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 1.3Nov 1, 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, alpha skeletal muscle
B: Twinfilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9954
Polymers61,4482
Non-polymers5472
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-25 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.780, 72.990, 168.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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) / References: UniProt: P68135
#2: Protein Twinfilin-1 / Protein A6


Mass: 19350.977 Da / Num. of mol.: 1 / Fragment: C-terminal domain, ADF-H 2, UNP RESIDUES 167-322 / Mutation: V168M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Twf1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q91YR1
#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 / Adenosine triphosphate


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


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM Tris pH 7.5, 50mM NaCl, 0.2mM ATP, 0.2mM DTT, 0.2mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07225 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2007 / Details: toroidal mirror
RadiationMonochromator: Si (1,1,1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07225 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 26755 / Num. obs: 26755 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 9.6
Reflection shellResolution: 2.55→2.61 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1318 / Rsym value: 0.552 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HD7, 2A42

2hd7

2a42


Resolution: 2.55→42.76 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.881 / SU B: 12.415 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R: 0.563 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27925 1125 5.1 %RANDOM
Rwork0.20821 ---
obs0.21199 20748 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.293 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--0.16 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.55→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 32 123 4211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224175
X-RAY DIFFRACTIONr_bond_other_d0.0010.022838
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9765659
X-RAY DIFFRACTIONr_angle_other_deg0.95936928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6365510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47824.096188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14315732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1871526
X-RAY DIFFRACTIONr_chiral_restr0.0910.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02827
X-RAY DIFFRACTIONr_nbd_refined0.2210.2985
X-RAY DIFFRACTIONr_nbd_other0.1990.23044
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21995
X-RAY DIFFRACTIONr_nbtor_other0.090.22257
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2138
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1330.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5561.52652
X-RAY DIFFRACTIONr_mcbond_other0.0831.51029
X-RAY DIFFRACTIONr_mcangle_it0.96224137
X-RAY DIFFRACTIONr_scbond_it1.21431769
X-RAY DIFFRACTIONr_scangle_it1.8514.51522
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 81 -
Rwork0.304 1513 -
obs--99.87 %

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