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- PDB-3a5l: Crystal Structure of a Dictyostelium P109A Mg2+-Actin in Complex ... -

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Basic information

Entry
Database: PDB / ID: 3a5l
TitleCrystal Structure of a Dictyostelium P109A Mg2+-Actin in Complex with Human Gelsolin Segment 1
Components
  • Gelsolin
  • Major actin
KeywordsCONTRACTILE PROTEIN / ACTIN / ADP / HYDROLYSIS / ACTIN CAPPING / ACTIN-BINDING / CYTOSKELETON / ATP-BINDING / NUCLEOTIDE-BINDING / STRUCTURAL PROTEIN
Function / homology
Function and homology information


intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / cell pole / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering ...intranuclear rod / phototaxis / leading edge of lamellipodium / macropinocytic cup / phagolysosome / cell pole / 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 / plasma membrane repair / actin filament severing / actin filament capping / actin filament depolymerization / early phagosome / actin polymerization or depolymerization / barbed-end actin filament capping / hyperosmotic response / cell projection assembly / cardiac muscle cell contraction / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / podosome / myosin binding / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / cell leading edge / pseudopodium / mitotic cytokinesis / phagocytic cup / endocytic vesicle / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytosis / phagocytic vesicle / phosphatidylinositol-4,5-bisphosphate binding / vesicle-mediated transport / response to cAMP / response to muscle stretch / actin filament polymerization / lipid droplet / 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 / cell morphogenesis / cellular response to type II interferon / structural constituent of cytoskeleton / endocytosis / chemotaxis / actin filament binding / cell-cell junction / actin cytoskeleton / lamellipodium / actin binding / cell cortex / secretory granule lumen / blood microparticle / ficolin-1-rich granule lumen / amyloid fibril formation / 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'-DIPHOSPHATE / Gelsolin / Major actin
Similarity search - Component
Biological speciesHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMurakami, K. / Yasunaga, T. / Noguchi, T.Q. / Uyeda, T.Q. / Wakabayashi, T.
CitationJournal: Cell / Year: 2010
Title: Structural basis for actin assembly, activation of ATP hydrolysis, and delayed phosphate release.
Authors: Kenji Murakami / Takuo Yasunaga / Taro Q P Noguchi / Yuki Gomibuchi / Kien X Ngo / Taro Q P Uyeda / Takeyuki Wakabayashi /
Abstract: Assembled actin filaments support cellular signaling, intracellular trafficking, and cytokinesis. ATP hydrolysis triggered by actin assembly provides the structural cues for filament turnover in vivo. ...Assembled actin filaments support cellular signaling, intracellular trafficking, and cytokinesis. ATP hydrolysis triggered by actin assembly provides the structural cues for filament turnover in vivo. Here, we present the cryo-electron microscopic (cryo-EM) structure of filamentous actin (F-actin) in the presence of phosphate, with the visualization of some α-helical backbones and large side chains. A complete atomic model based on the EM map identified intermolecular interactions mediated by bound magnesium and phosphate ions. Comparison of the F-actin model with G-actin monomer crystal structures reveals a critical role for bending of the conserved proline-rich loop in triggering phosphate release following ATP hydrolysis. Crystal structures of G-actin show that mutations in this loop trap the catalytic site in two intermediate states of the ATPase cycle. The combined structural information allows us to propose a detailed molecular mechanism for the biochemical events, including actin polymerization and ATPase activation, critical for actin filament dynamics.
History
DepositionAug 9, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
S: Gelsolin
C: Major actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1696
Polymers55,6372
Non-polymers5324
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-53 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.852, 69.005, 180.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules SC

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


Mass: 14205.001 Da / Num. of mol.: 1 / Fragment: GELSOLIN-LIKE 1, residues 53-176 / Mutation: N35C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PTIKL / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#2: Protein Major actin / Actin-1 / Actin-2 / Actin-2-sub 1 / Actin-4 / Actin-5 / Actin-6 / Actin-7 / Actin-8 / Actin A8 / ...Actin-1 / Actin-2 / Actin-2-sub 1 / Actin-4 / Actin-5 / Actin-6 / Actin-7 / Actin-8 / Actin A8 / Actin-IEL1 / Actin-9 / Actin-11 / Actin-12 / Actin A12 / Actin-13 / Actin-14 / Actin-15 / Actin A1 / Actin III / Actin-3a / Actin-16 / Actin M6 / Actin-19 / Actin-20 / Actin-21


Mass: 41432.203 Da / Num. of mol.: 1 / Mutation: P109A/E205A/R206A/E207A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: DICTYOSTELIUM (eukaryote) / References: UniProt: P07830

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Non-polymers , 4 types, 297 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 3.19 Å3/Da / Density % sol: 61.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 28588 / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.39→2.49 Å / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 13.92

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A5N

3a5n


Resolution: 2.4→48.13 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0 / SU B: 5.884 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.288 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1432 5 %RANDOM
Rwork0.189 26978 --
obs0.19 28410 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.49 Å2 / Biso mean: 37.333 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---2.29 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 30 293 4113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223900
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.9725288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47624.035171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48615641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.7161521
X-RAY DIFFRACTIONr_chiral_restr0.120.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022964
X-RAY DIFFRACTIONr_nbd_refined0.2280.21845
X-RAY DIFFRACTIONr_nbtor_refined0.3170.22626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2271
X-RAY DIFFRACTIONr_metal_ion_refined0.1350.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.217
X-RAY DIFFRACTIONr_mcbond_it1.5881.52458
X-RAY DIFFRACTIONr_mcangle_it2.27123869
X-RAY DIFFRACTIONr_scbond_it3.79231637
X-RAY DIFFRACTIONr_scangle_it5.0974.51419
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 97 -
Rwork0.215 1909 -
all-2006 -
obs--96.49 %

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