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- PDB-1h1v: gelsolin G4-G6/actin complex -

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Basic information

Entry
Database: PDB / ID: 1h1v
Titlegelsolin G4-G6/actin complex
Components
  • ACTIN
  • GELSOLIN
KeywordsACTIN-BINDING / SEVERING / CAPPING / CALCIUM / AMYLOID / MUSCLE CONTRACTION
Function / homologyADF-H/Gelsolin-like domain superfamily / Neutrophil degranulation / Gelsolin repeat / Actin / Gelsolin / Actin family / Actins signature 2. / Actins and actin-related proteins signature. / Caspase-mediated cleavage of cytoskeletal proteins / Actin, conserved site ...ADF-H/Gelsolin-like domain superfamily / Neutrophil degranulation / Gelsolin repeat / Actin / Gelsolin / Actin family / Actins signature 2. / Actins and actin-related proteins signature. / Caspase-mediated cleavage of cytoskeletal proteins / Actin, conserved site / Amyloid fiber formation / Actins signature 1. / Actin/actin-like conserved site / Villin/Gelsolin / Gelsolin-like domain / Striated Muscle Contraction / skeletal muscle fiber adaptation / response to extracellular stimulus / regulation of receptor clustering / regulation of plasma membrane raft polarization / striated muscle atrophy / regulation of establishment of T cell polarity / renal protein absorption / positive regulation of keratinocyte apoptotic process / 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 / cellular response to organonitrogen compound / 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 / response to lithium ion / 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 / sarcomere / filopodium / actin filament / cellular response to interferon-gamma / phosphatidylinositol-mediated signaling / ruffle / protein destabilization / response to mechanical stimulus / phagocytosis, engulfment / cellular response to cadmium ion / calcium-dependent protein binding / response to steroid hormone / 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 / protein-containing complex / extracellular space / extracellular exosome
Function and homology information
Specimen sourceHOMO SAPIENS (human)
ORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 2.99 Å resolution
AuthorsChoe, H. / Burtnick, L.D. / Mejillano, M. / Yin, H.L. / Robinson, R.C. / Choe, S.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: The Calcium Activation of Gelsolin:Insights from the 3A Structure of the G4-G6/Actin Complex
Authors: Choe, H. / Burtnick, L.D. / Mejillano, M. / Yin, H.L. / Robinson, R.C. / Choe, S.
#1: Journal: Science / Year: 1999
Title: Domain Movement in Gelsolin: A Calcium-Activated Switch
Authors: Choe, H. / Burtnick, L.D. / Mejillano, M. / Yin, H.L. / Robinson, R.C. / Choe, S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 23, 2002 / Release: Jan 24, 2003
RevisionDateData content typeGroupProviderType
1.0Jan 24, 2003Structure modelrepositoryInitial release
1.1Jun 2, 2011Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACTIN
G: GELSOLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9788
Polyers78,2702
Non-polymers7086
Water6,233346
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)54.350, 113.450, 159.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21
DetailsTHE COMPLEX IS A HETERODIMER WITH ONE MOLECULE OF ACTINAND ONE MOLECULE OF GELSOLIN.

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Components

#1: Protein/peptide ACTIN /


Mass: 41862.613 Da / Num. of mol.: 1 / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: MUSCLE / References: UniProt: P02568, UniProt: P68135*PLUS
#2: Protein/peptide GELSOLIN / / ACTIN-DEPOLYMERIZING FACTOR / BREVIN / AGEL


Mass: 36407.551 Da / Num. of mol.: 1 / Fragment: G4-G6, RESIDUES 412-742 OF CYTOPLASMIC ISOFORM / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P06396
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / 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.: 346 / Formula: H2O / Water
Compound detailsGELSOLIN: CALCIUM-REGULATED, ACTIN-MODULATING PROTEIN THAT BINDS TO ACTIN MONOMERS OR FILAMENTS AT ...GELSOLIN: CALCIUM-REGULATED, ACTIN-MODULATING PROTEIN THAT BINDS TO ACTIN MONOMERS OR FILAMENTS AT THE BARBED END. ACTIN: HIGHLY CONSERVED PROTEINS INVOLVED IN CELL MOTILITY AND EXPRESSED IN ALL EUKARYOTIC CELLS.
Sequence detailsSWISSPROT HAS MERGED THE SEQUENCE OF RABBIT, HUMAN PIG, RAT AND MOUSE ACTIN AND GIVEN THE SWISSPROT ID P02568.

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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: 3.14 / Density percent sol: 60.81 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 100MM HEPES BUFFER, PH 7.5, 20% GLYCEROL, 10 % PEG 8000
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 8 / Method: vapor diffusion / Details: Robinson, R.C., (1999) Science, 286, 1939.
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDDetailsChemical formula
15 mMTris-HCldroppH8.0
20.2 mMATPdrop
30.1 mMdropCaCl2
40.5 mMdithiothreitoldrop
510 mg/mlproteindrop
610 %PEG8000reservoir
720 %glycerolreservoir
8100 mMHEPESreservoir

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Data collection

DiffractionMean temperature: 95
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL9-2 / Synchrotron site: SSRL / Beamline: BL9-2 / Wavelength: 1.07
DetectorDetector: CCD
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 / Relative weight: 1
ReflectionD resolution high: 3 / D resolution low: 2 / Number obs: 20076 / Observed criterion sigma I: 0 / Rmerge I obs: 0.074 / NetI over sigmaI: 8.2 / Redundancy: 4.3 % / Percent possible obs: 98
Reflection shellRmerge I obs: 0.3
Reflection
*PLUS
D resolution low: 2 / Percent possible obs: 98

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefineMethod to determine structure: MAD
Starting model: PDB ENTRY 1DB0
Overall SU B: 24.358 / Overall SU ML: 0.464 / R Free selection details: RANDOM / Cross valid method: THOUGHOUT / Overall ESU R Free: 0.45
Displacement parametersB iso mean: 26.173 / Aniso B11: 0.01 / Aniso B12: 0 / Aniso B13: 0 / Aniso B22: 0.01 / Aniso B23: 0 / Aniso B33: -0.02
Least-squares processR factor R free: 0.268 / R factor R work: 0.219 / Highest resolution: 2.99 / Lowest resolution: 19.73 / Number reflection R free: 1010 / Number reflection obs: 19066 / Percent reflection R free: 5 / Percent reflection obs: 1
Refine hist #LASTHighest resolution: 2.99 / Lowest resolution: 19.73
Number of atoms included #LASTProtein: 5414 / Nucleic acid: 0 / Ligand: 36 / Solvent: 346 / Total: 5796
Least-squares process
*PLUS
Highest resolution: 3 / Lowest resolution: 2
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.58
Refine LS shell
*PLUS
Highest resolution: 2.994 / Total number of bins used: 20 / Lowest resolution: 3.07 / Number reflection R work: 1141 / Percent reflection R free: 65 / R factor R free: 0.414 / R factor R work: 0.295

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