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- PDB-3cip: Complex of Dictyostelium Discoideum Actin with Gelsolin -

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Basic information

Entry
Database: PDB / ID: 3cip
TitleComplex of Dictyostelium Discoideum Actin with Gelsolin
Components
  • Gelsolin
  • Major actin
KeywordsSTRUCTURAL PROTEIN / Actin / Gelsolin / Dictyostelium discoideum / Actin-Associated Protein / Methyl Histidine / ATP-binding / Cytoskeleton / Nucleotide-binding / Phosphoprotein / Actin capping / Actin-binding / Alternative initiation / Amyloid / Disease mutation / Secreted
Function / homology
Function and homology information


intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / cell pole ...intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / cell pole / 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 / regulation of podosome assembly / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / barbed-end actin filament capping / plasma membrane repair / actin filament depolymerization / actin filament capping / actin polymerization or depolymerization / cell projection assembly / early phagosome / hyperosmotic response / cardiac muscle cell contraction / Sensory processing of sound by outer hair cells of the cochlea / podosome / relaxation of cardiac muscle / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / myosin binding / cell leading edge / pseudopodium / mitotic cytokinesis / sarcoplasm / endocytic vesicle / cilium assembly / phagocytic cup / Caspase-mediated cleavage of cytoskeletal proteins / phagocytosis / response to cAMP / vesicle-mediated transport / phagocytic vesicle / lipid droplet / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / central nervous system development / actin filament organization / actin filament / protein destabilization / cell morphogenesis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / cellular response to type II interferon / endocytosis / chemotaxis / actin filament binding / cell-cell junction / lamellipodium / actin cytoskeleton / actin binding / cell cortex / secretory granule lumen / blood microparticle / amyloid fibril formation / ficolin-1-rich granule lumen / hydrolase activity / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Major actin
Similarity search - Component
Biological speciesHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsBaek, K. / Dominguez, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Modulation of actin structure and function by phosphorylation of Tyr-53 and profilin binding.
Authors: Baek, K. / Liu, X. / Ferron, F. / Shu, S. / Korn, E.D. / Dominguez, R.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major actin
G: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,71117
Polymers55,9992
Non-polymers1,71215
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-135.6 kcal/mol
Surface area20900 Å2
MethodPISA
2
A: Major actin
G: Gelsolin
hetero molecules

A: Major actin
G: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,42234
Polymers111,9974
Non-polymers3,42530
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13060 Å2
ΔGint-320.3 kcal/mol
Surface area39930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.881, 69.172, 56.564
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-406-

SO4

21A-409-

SO4

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein Major actin


Mass: 41660.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: P07830
#2: Protein Gelsolin / Actin-depolymerizing factor / ADF / Brevin / AGEL


Mass: 14338.106 Da / Num. of mol.: 1 / Fragment: Gelsolin Segment 1 (UNP RESIDUES 52-176)
Source method: isolated from a genetically manipulated source
Details: Intein fusion. Additional Ala-Gly-His at N-terminus after removing fusion tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: gsn / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06396

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Non-polymers , 6 types, 476 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 3.03 Å3/Da / Density % sol: 59.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, pH7.5, 1.7M Li2SO4, 2mM ATP, 1mM EDTA, 5% Glycerol, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.9999 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 15, 2007 / Details: 1-m Pt/Pd-coated ULE mirror
RadiationMonochromator: 1-m Pt/Pd-coated ULE mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 88709 / Num. obs: 85829 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 36.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.521 / % possible all: 78.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.72 Å
Translation2.5 Å43.72 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NM1

1nm1


Resolution: 1.6→43.73 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.115 / SU ML: 0.049 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19739 4322 5 %RANDOM
Rwork0.1497 ---
obs0.15211 81476 96.66 %-
all-88763 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.242 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.03 Å2
2---0.04 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 96 461 4412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224227
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9855781
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0355547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38224.043188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23215719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0721523
X-RAY DIFFRACTIONr_chiral_restr0.0920.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023201
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21993
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22873
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2407
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.22622603
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.34834115
X-RAY DIFFRACTIONr_scbond_it5.54641853
X-RAY DIFFRACTIONr_scangle_it7.09161635
X-RAY DIFFRACTIONr_rigid_bond_restr3.30234456
X-RAY DIFFRACTIONr_sphericity_free11.3353463
X-RAY DIFFRACTIONr_sphericity_bonded8.13634111
LS refinement shellResolution: 1.596→1.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 250 -
Rwork0.23 4668 -
obs--75.67 %

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