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- PDB-1mdu: Crystal structure of the chicken actin trimer complexed with huma... -

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Basic information

Entry
Database: PDB / ID: 1mdu
TitleCrystal structure of the chicken actin trimer complexed with human gelsolin segment 1 (GS-1)
Components
  • a-actin
  • gelsolin precursor
KeywordsSTRUCTURAL PROTEIN / gelsolin precursor / a-actin / ADENOSINE-5'-TRIPHOSPHATE / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1 / 3-DIOL
Function / homology
Function and homology information


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 / phosphatidylinositol 3-kinase catalytic subunit binding ...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 / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / regulation of podosome assembly / Striated Muscle Contraction / 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 / phagocytosis, engulfment / cortical actin cytoskeleton / hepatocyte apoptotic process / skeletal muscle thin filament assembly / striated muscle thin filament / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / stress fiber / skeletal muscle fiber development / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / 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 / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / 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
Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / 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 2 / Actin; Chain A, domain 2 / 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 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Gelsolin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDawson, J.F. / Sablin, E.P. / Spudich, J.A. / Fletterick, R.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of an F-actin trimer disrupted by gelsolin and implications for the mechanism of severing
Authors: Dawson, J.F. / Sablin, E.P. / Spudich, J.A. / Fletterick, R.J.
History
DepositionAug 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: gelsolin precursor
B: a-actin
D: gelsolin precursor
E: a-actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,78114
Polymers112,3644
Non-polymers1,41710
Water8,485471
1
A: gelsolin precursor
B: a-actin
hetero molecules

A: gelsolin precursor
B: a-actin
hetero molecules

A: gelsolin precursor
B: a-actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,91424
Polymers168,5456
Non-polymers2,36918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
2
D: gelsolin precursor
E: a-actin
hetero molecules

D: gelsolin precursor
E: a-actin
hetero molecules

D: gelsolin precursor
E: a-actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,42818
Polymers168,5456
Non-polymers1,88212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
crystal symmetry operation2_556-x,y+1/2,-z+11
Unit cell
Length a, b, c (Å)67.187, 75.942, 96.747
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two actin:GS-1 protomers from two different actin:GS-1 trimers. The biological assembly (actin:GS-1 trimer) is generated by applying the following symmetry operators to chains A, B, C (and G for solvent molecules): 1) x, y, z; 2) -x+1, y-1/2, -z; 3) -x+1, y+1/2, -z

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Components

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Protein , 2 types, 4 molecules ADBE

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


Mass: 14071.831 Da / Num. of mol.: 2 / Fragment: actin-severing
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06396
#2: Protein a-actin


Mass: 42109.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139

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Non-polymers , 4 types, 481 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.2 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, tris, calcium chloride, magnesium chloride, ADP, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
215 %(w/v)PEG10001reservoir
325 mMTris-HCl1reservoirpH8.0
42 mMATP1reservoir
5100 mM1reservoirMgCl2
62 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2002
RadiationMonochromator: double-crystal Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 49210 / Num. obs: 45313 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 17
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 2 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 5.5 / Num. unique all: 6687 / Rsym value: 0.164 / % possible all: 81.8
Reflection
*PLUS
Redundancy: 4 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 81.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ESV

1esv


Resolution: 2.2→25 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Missing residues and atoms are due to disorder and absent electron density in electron density maps.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2278 -random
Rwork0.193 ---
all0.207 49210 --
obs0.207 45313 91.4 %-
Solvent computationSolvent model: bulk solvent / Bsol: 56.5848 Å2 / ksol: 0.361737 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-14.21 Å20 Å27.02 Å2
2---7.81 Å20 Å2
3----6.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7611 0 77 471 8159
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d1.34
X-RAY DIFFRACTIONc_mcbond_it1.881.5
X-RAY DIFFRACTIONc_mcangle_it2.792
X-RAY DIFFRACTIONc_scbond_it3.932
X-RAY DIFFRACTIONc_scangle_it5.162.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.314 349 -
Rwork0.284 --
obs-6687 81.8 %
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.34

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