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

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Basic information

Entry
Database: PDB / ID: 1eqy
TitleCOMPLEX BETWEEN RABBIT MUSCLE ALPHA-ACTIN: HUMAN GELSOLIN DOMAIN 1
Components
  • ALPHA ACTIN
  • GELSOLIN
KeywordsCONTRACTILE PROTEIN / gelsolin / actin
Function / homology
Function and homology information


renal protein absorption / regulation of establishment of T cell polarity / striated muscle atrophy / positive regulation of keratinocyte apoptotic process / regulation of plasma membrane raft polarization / regulation of receptor clustering / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / actin cap / sequestering of actin monomers ...renal protein absorption / regulation of establishment of T cell polarity / striated muscle atrophy / positive regulation of keratinocyte apoptotic process / regulation of plasma membrane raft polarization / regulation of receptor clustering / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / actin cap / 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 / actin filament capping / tissue regeneration / oligodendrocyte development / positive regulation of actin-dependent ATPase activity / mesenchyme migration / response to folic acid / tropomyosin binding / cortical actin cytoskeleton / myosin heavy chain binding / troponin I binding / podosome / skeletal muscle thin filament assembly / actin filament bundle / striated muscle thin filament / filamentous actin / hepatocyte apoptotic process / cilium assembly / actin monomer binding / skeletal muscle fiber development / skeletal muscle myofibril / regulation of cell adhesion / actin filament bundle assembly / stress fiber / titin binding / phagocytic vesicle / actin filament polymerization / actin filament reorganization / actin filament / filopodium / cellular response to interferon-gamma / phosphatidylinositol-mediated signaling / ruffle / phagocytosis, engulfment / protein destabilization / cellular response to cadmium ion / cell body / calcium-dependent protein binding / actin cytoskeleton / actin filament binding / lamellipodium / myelin sheath / actin binding / amyloid fibril formation / secretory granule lumen / ficolin-1-rich granule lumen / response to ethanol / blood microparticle / aging / 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 / protein-containing complex / cell / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Actin/actin-like conserved site / Gelsolin-like domain / ADF-H/Gelsolin-like domain superfamily / Gelsolin / Actin family / Actin / Gelsolin repeat / Actin, conserved site / Villin/Gelsolin / Actin; Chain A, domain 2 ...Actin/actin-like conserved site / Gelsolin-like domain / ADF-H/Gelsolin-like domain superfamily / Gelsolin / Actin family / Actin / Gelsolin repeat / Actin, conserved site / Villin/Gelsolin / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Severin / Severin / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Gelsolin / Actin, alpha skeletal muscle
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
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
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: GELSOLIN
A: ALPHA ACTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7986
Polymers56,1712
Non-polymers6274
Water11,440635
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-53 kcal/mol
Surface area20610 Å2
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-MP212121

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Components

#1: Protein GELSOLIN /


Mass: 14060.871 Da / Num. of mol.: 1 / Fragment: DOMAIN 1 / Mutation: N33C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: PLASMA / Plasmid: PMW172 / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#2: Protein ALPHA ACTIN


Mass: 42109.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P68135
#3: Chemical ChemComp-CA / CALCIUM ION / Calcium


Mass: 40.078 Da / Num. of mol.: 3 / 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.: 635 / 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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 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
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.911
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 19, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911 Å / Relative weight: 1
ReflectionResolution: 2.3→15.4 Å / Num. obs: 28998 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 5.7
Reflection shellResolution: 2.33→2.46 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.21 / % possible all: 66
Reflection shell
*PLUS
% possible obs: 66 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4(TRUNCATE)data scaling
X-PLORphasing
RefinementResolution: 2.3→15.4 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.28 1474 -
Rwork0.174 --
Obs0.174 28975 100 %
All-28975 -
Refinement stepCycle: LAST / Resolution: 2.3→15.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 34 635 4486
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d1.54

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