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- PDB-1nlv: Crystal Structure Of Dictyostelium Discoideum Actin Complexed Wit... -

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Basic information

Entry
Database: PDB / ID: 1nlv
TitleCrystal Structure Of Dictyostelium Discoideum Actin Complexed With Ca ATP And Human Gelsolin Segment 1
Components
  • Actin
  • Gelsolin
KeywordsSTRUCTURAL PROTEIN / actin / gelsolin / cytoskeleton / cell motility
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 / renal protein absorption ...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 / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / cell pole / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / myosin II binding / host-mediated suppression of symbiont invasion / actin filament severing / plasma membrane repair / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / cell projection assembly / actin polymerization or depolymerization / early phagosome / cardiac muscle cell contraction / hyperosmotic response / relaxation of cardiac muscle / Sensory processing of sound by outer hair cells of the cochlea / podosome / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / myosin binding / pseudopodium / cell leading edge / mitotic cytokinesis / sarcoplasm / endocytic vesicle / cilium assembly / response to cAMP / Caspase-mediated cleavage of cytoskeletal proteins / phagocytosis / phagocytic cup / vesicle-mediated transport / phagocytic vesicle / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / lipid droplet / actin filament organization / central nervous system development / actin filament / protein destabilization / cellular response to type II interferon / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endocytosis / cell morphogenesis / 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 / cytoplasm / cytosol
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 / SULFUR DIOXIDE / Major actin / Gelsolin / Major actin
Similarity search - Component
Biological speciesHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVorobiev, S.M. / Welti, S. / Condeelis, J. / Almo, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The Structure of Non-Vertebrate Actin: Implications For The ATP Hydrolytic Mechanism
Authors: Vorobiev, S.M. / Strokopytov, B. / Drubin, D.G. / Frieden, C. / Ono, S. / Condeelis, J. / Rubenstein, P.A. / Almo, S.C.
History
DepositionJan 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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_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.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.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_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_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
A: Actin
G: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5638
Polymers55,7192
Non-polymers8446
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-65 kcal/mol
Surface area19910 Å2
MethodPISA
2
A: Actin
G: Gelsolin
hetero molecules

A: Actin
G: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,12616
Polymers111,4384
Non-polymers1,68712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8930 Å2
ΔGint-143 kcal/mol
Surface area38210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.446, 69.089, 56.570
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-524-

HOH

21A-544-

HOH

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Components

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Protein , 2 types, 2 molecules AG

#1: Protein Actin


Mass: 41647.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Dictyostelium discoideum (eukaryote) / References: UniProt: P02577, UniProt: P07830*PLUS
#2: Protein Gelsolin / Actin-depolymerizing factor / ADF / Brevin / AGEL


Mass: 14071.831 Da / Num. of mol.: 1 / Fragment: DOMAIN 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Plasmid: pMW172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06396

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Non-polymers , 5 types, 337 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 59.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: lithium chloride, magnesium chloride, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.07018 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07018 Å / Relative weight: 1
ReflectionResolution: 1.8→23 Å / Num. all: 61207 / Num. obs: 61207 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.14 %
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.338 / Num. unique all: 6067 / % possible all: 99.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DAG

1dag


Resolution: 1.8→23 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2584 -RANDOM
Rwork0.2097 --
obs-61205 -
Refinement stepCycle: LAST / Resolution: 1.8→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 46 331 4146

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