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- PDB-3m1f: Crosslinked complex of actin with first W domain of Vibrio paraha... -

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Basic information

Entry
Database: PDB / ID: 3m1f
TitleCrosslinked complex of actin with first W domain of Vibrio parahaemolyticus VopL
Components
  • Actin, alpha skeletal muscle
  • Putative uncharacterized protein VPA1370
KeywordsCONTRACTILE PROTEIN / ACTIN / ACTIN-BINDING PROTEIN / CROSSLINKING / NUCLEATOR / PROTEIN-PROTEIN INTERACTION / ATP-binding / Cytoskeleton / Methylation / Muscle protein / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / 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 / actin binding / 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
: / : / VopL C-terminal dimerization domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain / WH2 domain profile. / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain ...: / : / VopL C-terminal dimerization domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain / WH2 domain profile. / 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 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle / WH2 domain-containing protein
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Vibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsNamgoong, 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 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 2, 2014Group: Other
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
V: Putative uncharacterized protein VPA1370
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8504
Polymers45,3032
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-33 kcal/mol
Surface area17280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.606, 76.363, 86.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

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


Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein/peptide Putative uncharacterized protein VPA1370 / VopL


Mass: 3426.897 Da / Num. of mol.: 1 / Fragment: VopL WH2 domain (130-160aa) / Mutation: V131C / Source method: obtained synthetically
Details: Chemically synthesized peptide. The sequence naturally occurs in Vibrio parahaemolyticus.
Source: (synth.) Vibrio parahaemolyticus (bacteria) / References: UniProt: Q87GE5
#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.2 N Lithium Nitrate, 20% polyethylene glycol 3350, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. all: 18692 / Num. obs: 10207 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 12.9 % / Biso Wilson estimate: 62.01 Å2 / Rmerge(I) obs: 0.168 / Rsym value: 0.168 / Net I/σ(I): 16.3
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.461 / % possible all: 92.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.autoMR)model building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2a3z

2a3z


Resolution: 2.89→37.51 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 929 -RANDOM
Rwork0.212 ---
obs0.212 9283 90.13 %-
all-9283 --
Displacement parametersBiso mean: 62.9 Å2
Refinement stepCycle: LAST / Resolution: 2.89→37.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 32 0 3058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr

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