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- PDB-1nmd: Crystal Structure of D. Discoideum Actin-Gelsolin Segment 1 Compl... -

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Basic information

Entry
Database: PDB / ID: 1nmd
TitleCrystal Structure of D. Discoideum Actin-Gelsolin Segment 1 Complex Crystallized In Presence Of Lithium ATP
Components
  • Actin
  • Gelsolin
KeywordsSTRUCTURAL PROTEIN / ACTIN / GELSOLIN / CYTOSKELETON ORGANIZATION / ACTIN-ASSOCIATED PROTEIN
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 polymerization or depolymerization / actin filament capping / 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 / cortical actin cytoskeleton / phagocytosis, engulfment / myosin binding / hepatocyte apoptotic process / cell leading edge / pseudopodium / mitotic cytokinesis / phagocytic cup / sarcoplasm / endocytic vesicle / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytosis / response to cAMP / phagocytic vesicle / vesicle-mediated transport / : / response to muscle stretch / lipid droplet / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / actin filament organization / central nervous system development / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / cell morphogenesis / structural constituent of cytoskeleton / cellular response to type II interferon / endocytosis / chemotaxis / actin filament binding / cell-cell junction / actin cytoskeleton / lamellipodium / 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 / SULFUR DIOXIDE / Major actin / Gelsolin / Major actin
Similarity search - Component
Biological speciesHomo sapiens (human)
Dictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVorobiev, S.M. / Welti, S. / Condeelis, J. / Almo, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The Structure Of The 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 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 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)56,4276
Polymers55,7192
Non-polymers7074
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-41 kcal/mol
Surface area19930 Å2
MethodPISA
2
A: Actin
G: Gelsolin
hetero molecules

A: Actin
G: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,85312
Polymers111,4384
Non-polymers1,4158
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8120 Å2
ΔGint-94 kcal/mol
Surface area38300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.912, 69.053, 56.613
Angle α, β, γ (deg.)90.00, 104.65, 90.00
Int Tables number5
Space group name H-MC121

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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 I
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, 367 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-SO2 / SULFUR DIOXIDE


Mass: 64.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2S
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 363 / 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: 59.47 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Lithium sulfate, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 52529 / Num. obs: 52529 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.61 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.365 / Num. unique all: 2529 / % possible all: 96.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DGA

1dga
PDB Unreleased entry


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2504 -RANDOM
Rwork0.2028 --
all-52524 -
obs-52524 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 40 363 4162
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.403

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