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- PDB-3m3n: Structure of a Longitudinal Actin Dimer Assembled by Tandem W Domains -

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Basic information

Entry
Database: PDB / ID: 3m3n
TitleStructure of a Longitudinal Actin Dimer Assembled by Tandem W Domains
Components
  • Actin, alpha skeletal muscle
  • Neural Wiskott-Aldrich syndrome protein
KeywordsSTRUCTURAL PROTEIN / actin dimer / ATP-binding / actin cytoskeleton / methylation / muscle protein / actin-binding / MOTOR PROTEIN
Function / homology
Function and homology information


negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / actin nucleation / vesicle transport along actin filament / positive regulation of smooth muscle cell differentiation / actin cap / vesicle organization / Platelet degranulation ...negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / negative regulation of lymphocyte migration / actin nucleation / vesicle transport along actin filament / positive regulation of smooth muscle cell differentiation / actin cap / vesicle organization / Platelet degranulation / negative regulation of actin filament polymerization / vesicle budding from membrane / dendritic spine morphogenesis / protein-containing complex localization / regulation of postsynapse organization / positive regulation of endothelial cell chemotaxis / positive regulation of filopodium assembly / cytoskeletal motor activator activity / positive regulation of smooth muscle cell migration / positive regulation of ATP biosynthetic process / myosin heavy chain binding / tropomyosin binding / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / positive regulation of blood vessel endothelial cell migration / stress fiber / skeletal muscle fiber development / tumor necrosis factor-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / titin binding / actin filament polymerization / protein sequestering activity / regulation of cell migration / actin filament organization / filopodium / actin filament / response to bacterium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of inflammatory response / calcium-dependent protein binding / lamellipodium / regulation of protein localization / actin binding / cell body / actin cytoskeleton organization / cytoplasmic vesicle / cytoskeleton / hydrolase activity / protein domain specific binding / cell division / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / glutamatergic synapse / enzyme binding / magnesium ion binding / positive regulation of transcription by RNA polymerase II / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Thymosin beta-4 family signature. / Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain ...Thymosin beta-4 family signature. / Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain / WH2 domain profile. / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB 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 / PH-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Thymosin beta-4 / Actin, alpha skeletal muscle / Actin nucleation-promoting factor WASL
Similarity search - Component
Biological speciesMus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7 Å
AuthorsRebowski, G. / Namgoong, S. / Dominguez, R.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of a longitudinal actin dimer assembled by tandem w domains: implications for actin filament nucleation.
Authors: Rebowski, G. / Namgoong, S. / Boczkowska, M. / Leavis, P.C. / Navaza, J. / Dominguez, R.
History
DepositionMar 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 6, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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 1.4Sep 6, 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: Actin, alpha skeletal muscle
W: Neural Wiskott-Aldrich syndrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9407
Polymers94,8463
Non-polymers1,0954
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.743, 100.743, 458.839
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 41875.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Neural Wiskott-Aldrich syndrome protein / N-WASP


Mass: 11094.438 Da / Num. of mol.: 1 / Fragment: Engineered tandem W domain construct 3W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wasl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91YD9, UniProt: P20065
#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 3.54 Å3/Da / Density % sol: 65.29 %
Crystal growTemperature: 300 K / pH: 10
Details: 100 mM CAPS pH 10.0, and 24% PEG 3350, 100 mM RbCl, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K

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Data collection

DiffractionMean temperature: 112 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 23, 2009
Details: CYLINDRICALLY BENT ULE GLASS MIRROR WITH PT AND PD COATINGS
RadiationMonochromator: CRYOGENICALLY-COOLED SI(111) DOUBLE-CRYSTAL SYSTEM
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7→50 Å / Num. obs: 2182 / % possible obs: 90 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.5
Reflection shellResolution: 7→7.25 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 1 / % possible all: 34.3

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M1F

3m1f


Resolution: 7→50 Å / Details: NO REFINEMENT WAS PERFORMED
Refinement stepCycle: LAST / Resolution: 7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5968 0 64 0 6032

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