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- PDB-1esv: COMPLEX BETWEEN LATRUNCULIN A:RABBIT MUSCLE ALPHA ACTIN:HUMAN GEL... -

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Basic information

Entry
Database: PDB / ID: 1esv
TitleCOMPLEX BETWEEN LATRUNCULIN A:RABBIT MUSCLE ALPHA ACTIN:HUMAN GELSOLIN DOMAIN 1
Components
  • ALPHA ACTIN
  • GELSOLIN
KeywordsCONTRACTILE PROTEIN / Latrunculin A / Gelsolin / Actin / Depolymerisation / Sequestration
Function / homologyADF-H/Gelsolin-like domain superfamily / Actins and actin-related proteins signature. / Villin/Gelsolin / Actin family / Gelsolin-like domain / Actins signature 1. / Gelsolin repeat / Actins signature 2. / Caspase-mediated cleavage of cytoskeletal proteins / Neutrophil degranulation ...ADF-H/Gelsolin-like domain superfamily / Actins and actin-related proteins signature. / Villin/Gelsolin / Actin family / Gelsolin-like domain / Actins signature 1. / Gelsolin repeat / Actins signature 2. / Caspase-mediated cleavage of cytoskeletal proteins / Neutrophil degranulation / Amyloid fiber formation / Gelsolin / Actin/actin-like conserved site / Actin / Actin, conserved site / striated muscle atrophy / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / positive regulation of protein processing in phagocytic vesicle / actin cap / positive regulation of actin nucleation / sequestering of actin monomers / regulation of podosome assembly / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / myosin II binding / sarcoplasm / negative regulation of viral entry into host cell / actin filament severing / actin nucleation / barbed-end actin filament capping / tissue regeneration / oligodendrocyte development / actin filament capping / positive regulation of actin-dependent ATPase activity / mesenchyme migration / cortical actin cytoskeleton / response to folic acid / tropomyosin binding / podosome / myosin heavy chain binding / troponin I binding / actin filament bundle / filamentous actin / hepatocyte apoptotic process / cilium assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / actin monomer binding / regulation of cell adhesion / actin filament bundle assembly / skeletal muscle myofibril / phagocytic vesicle / stress fiber / amyloid fibril formation / actin filament reorganization / titin binding / actin filament polymerization / filopodium / actin filament / cellular response to interferon-gamma / phosphatidylinositol-mediated signaling / ruffle / protein destabilization / phagocytosis, engulfment / cellular response to cadmium ion / calcium-dependent protein binding / cell body / actin cytoskeleton / actin filament binding / lamellipodium / actin binding / secretory granule lumen / response to ethanol / ficolin-1-rich granule lumen / blood microparticle / aging / myelin sheath / focal adhesion / protein domain specific binding / cellular protein metabolic process / positive regulation of gene expression / neutrophil degranulation / calcium ion binding / perinuclear region of cytoplasm / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm / Gelsolin / Actin, alpha skeletal muscle
Function and homology information
Specimen sourceHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2 Å resolution
AuthorsMorton, W.M. / Ayscough, K.A. / McLaughlin, P.J.
CitationJournal: Nat.Cell Biol. / Year: 2000
Title: Latrunculin alters the actin-monomer subunit interface to prevent polymerization.
Authors: Morton, W.M. / Ayscough, K.R. / McLaughlin, P.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 11, 2000 / Release: Jul 19, 2000
RevisionDateData content typeGroupProviderType
1.0Jul 19, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: GELSOLIN
A: ALPHA ACTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2207
Polyers56,1712
Non-polymers1,0495
Water7,999444
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4270
ΔGint (kcal/M)-56
Surface area (Å2)19620
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)56.750, 69.250, 182.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21
DetailsThe biological Assembly is a 1:1:1 complex between actin, gelsolin domain 1 and Latrunculin A

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Components

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Protein/peptide , 2 types, 2 molecules SA

#1: Protein/peptide GELSOLIN /


Mass: 14060.871 Da / Num. of mol.: 1 / Fragment: DOMAIN 1 / Mutation: N33C / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Cell: PLASMA / Plasmid name: PMW172 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#2: Protein/peptide ALPHA ACTIN


Mass: 42109.973 Da / Num. of mol.: 1 / Source: (natural) Oryctolagus cuniculus (rabbit) / Genus: Oryctolagus / Tissue: MUSCLE / References: UniProt: P68135

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Non-polymers , 4 types, 449 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Formula: Ca / Calcium
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / 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.: 1 / Formula: C22H31NO5S / Latrunculin
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Formula: H2O / Water

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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: 3.2 / Density percent sol: 61.54 %
Crystal growTemp: 298 K / Method: vapor diffusion / pH: 6.6
Details: PEG 6000, sodium Chloride, adenosine triphosphate, calcium, magnesium, sodium azide, pH 6.6, VAPOR DIFFUSION, temperature 298.0K
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion, hanging drop / Details: or 20 degrees centigrade
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
110 mg/mlprotein1drop
25-9 %(w/v)PEG60001reservoir

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Data collection

DiffractionMean temperature: 1
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX9.6 / Synchrotron site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC / Detector: CCD / Collection date: Feb 28, 1998
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 / Relative weight: 1
ReflectionB iso Wilson estimate: 28.8 / D resolution high: 2 / D resolution low: 25.7 / Number all: 42367 / Number obs: 42367 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.066 / NetI over sigmaI: 7.2 / Redundancy: 2.8 % / Percent possible obs: 85.6
Reflection shellRmerge I obs: 0.31 / Highest resolution: 2 / Lowest resolution: 2.11 / Number unique all: 4808 / Redundancy: 1 % / Percent possible all: 68
Reflection shell
*PLUS
Percent possible obs: 68

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Processing

Software
NameVersionClassification
X-PLORmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefineSigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.286 / R factor R work: 0.228 / Highest resolution: 2 / Lowest resolution: 25.7 / Number reflection R free: 2309 / Number reflection all: 43426 / Number reflection obs: 43426 / Percent reflection obs: 85.6
Refine hist #LASTHighest resolution: 2 / Lowest resolution: 25.7
Number of atoms included #LASTProtein: 3669 / Nucleic acid: 0 / Ligand: 63 / Solvent: 444 / Total: 4176
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.006
X-RAY DIFFRACTIONs_bond_d0.021

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