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- PDB-1eqy: COMPLEX BETWEEN RABBIT MUSCLE ALPHA-ACTIN: HUMAN GELSOLIN DOMAIN 1 -

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Entry
Database: PDB / ID: 1eqy
TitleCOMPLEX BETWEEN RABBIT MUSCLE ALPHA-ACTIN: HUMAN GELSOLIN DOMAIN 1
Components
  • ALPHA ACTIN
  • GELSOLIN
KeywordsCONTRACTILE PROTEIN / gelsolin / actin
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 / 2.3 Å resolution
AuthorsMcLaughlin, P.J. / Gooch, J.T. / Mannherz, H.G. / Weeds, A.G.
CitationJournal: Nature / Year: 1993
Title: Structure of gelsolin segment 1-actin complex and the mechanism of filament severing.
Authors: McLaughlin, P.J. / Gooch, J.T. / Mannherz, H.G. / Weeds, A.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 6, 2000 / Release: May 3, 2000
RevisionDateData content typeGroupProviderType
1.0May 3, 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)56,7986
Polyers56,1712
Non-polymers6274
Water11,440635
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3460
ΔGint (kcal/M)-53
Surface area (Å2)20610
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)57.330, 70.880, 183.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 3.32 / Density percent sol: 62.94 %
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: 20 ℃
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
15-9 %PEG60001reservoir
20.15 M1reservoirNaCl
30.1 mMATP1reservoir
40.1 mM1reservoirMg2+
51 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 1
SourceSource: SYNCHROTRON / Type: EMBL/DESY, HAMBURG BEAMLINE X11 / Synchrotron site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.911
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Aug 19, 1996
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911 / Relative weight: 1
ReflectionB iso Wilson estimate: 31.5 / D resolution high: 2.3 / D resolution low: 15.4 / Number obs: 28998 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.092 / NetI over sigmaI: 5.7 / Redundancy: 3.3 % / Percent possible obs: 89.1
Reflection shellRmerge I obs: 0.21 / Highest resolution: 2.33 / Lowest resolution: 2.46 / Redundancy: 2.3 % / Percent possible all: 66
Reflection shell
*PLUS
Percent possible obs: 66

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Processing

Software
NameVersionClassification
X-PLORmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
X-PLORphasing
RefineSigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.28 / R factor R work: 0.174 / R factor obs: 0.174 / Highest resolution: 2.3 / Lowest resolution: 15.4 / Number reflection R free: 1474 / Number reflection all: 28975 / Number reflection obs: 28975 / Percent reflection obs: 100
Refine hist #LASTHighest resolution: 2.3 / Lowest resolution: 15.4
Number of atoms included #LASTProtein: 3817 / Nucleic acid: 0 / Ligand: 34 / Solvent: 635 / Total: 4486
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d1.54

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