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- PDB-2ff6: Crystal structure of Gelsolin domain 1:ciboulot domain 2 hybrid i... -

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Basic information

Entry
Database: PDB / ID: 2ff6
TitleCrystal structure of Gelsolin domain 1:ciboulot domain 2 hybrid in complex with actin
Components
  • Actin, alpha skeletal muscle
  • CG4944-PC, isoform C
  • Gelsolin
KeywordsSTRUCTURAL PROTEIN/CONTRACTILE PROTEIN / Protein-Protein complex / STRUCTURAL PROTEIN-CONTRACTILE PROTEIN COMPLEX
Function / homology
Function and homology information


larval central nervous system remodeling / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / regulation of podosome assembly / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / : ...larval central nervous system remodeling / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / regulation of podosome assembly / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / : / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / cell projection assembly / cardiac muscle cell contraction / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / podosome / cytoskeletal motor activator activity / phagocytosis, engulfment / cortical actin cytoskeleton / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / hepatocyte apoptotic process / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / skeletal muscle fiber development / stress fiber / phosphatidylinositol-4,5-bisphosphate binding / titin binding / response to muscle stretch / actin filament polymerization / filopodium / actin filament organization / central nervous system development / actin filament / protein destabilization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / brain development / cellular response to type II interferon / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell body / secretory granule lumen / blood microparticle / ficolin-1-rich granule lumen / amyloid fibril formation / cytoskeleton / hydrolase activity / protein domain specific binding / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat ...Beta-thymosin / Beta-thymosin superfamily / Thymosin beta-4 family / Thymosin beta actin-binding motif. / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Gelsolin / Actin, alpha skeletal muscle / Ciboulot, isoform C
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsAguda, A.H. / Xue, B. / Robinson, R.C.
CitationJournal: Structure / Year: 2006
Title: The Structural Basis of Actin Interaction with Multiple WH2/beta-Thymosin Motif-Containing Proteins
Authors: Aguda, A.H. / Xue, B. / Irobi, E. / Preat, T. / Robinson, R.C.
History
DepositionDec 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Gelsolin
H: CG4944-PC, isoform C
A: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4517
Polymers61,8243
Non-polymers6274
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.221, 69.373, 79.650
Angle α, β, γ (deg.)90.00, 95.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules GA

#1: Protein Gelsolin / Actin-depolymerizing factor / ADF / Brevin / AGEL


Mass: 16867.998 Da / Num. of mol.: 1 / Fragment: Gelsolin domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHis8-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#3: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P68135

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Protein/peptide , 1 types, 1 molecules H

#2: Protein/peptide CG4944-PC, isoform C


Mass: 3093.301 Da / Num. of mol.: 1 / Fragment: ciboulot domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: pHis8-3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IRS7

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Non-polymers , 3 types, 281 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7% PEG 3000, 0.1M Hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 16, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→79.31 Å / Num. all: 38456 / Num. obs: 36145 / % possible obs: 99.04 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.05→2.1 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→29.5 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.355 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23679 1939 5.1 %RANDOM
Rwork0.20233 ---
obs0.20406 36145 99.04 %-
all-38456 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.681 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20.8 Å2
2---1.02 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 34 277 4222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224034
X-RAY DIFFRACTIONr_angle_refined_deg1.0761.9555471
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0335493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31724.208183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65815682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5341522
X-RAY DIFFRACTIONr_chiral_restr0.0710.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023056
X-RAY DIFFRACTIONr_nbd_refined0.1820.21886
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2306
X-RAY DIFFRACTIONr_metal_ion_refined0.0940.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.214
X-RAY DIFFRACTIONr_mcbond_it0.7451.52546
X-RAY DIFFRACTIONr_mcangle_it0.92723976
X-RAY DIFFRACTIONr_scbond_it1.39831716
X-RAY DIFFRACTIONr_scangle_it2.0574.51495
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 156 -
Rwork0.234 2631 -
obs--98.24 %

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