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- PDB-3ffk: Crystal structure of human Gelsolin domains G1-G3 bound to Actin -

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Basic information

Entry
Database: PDB / ID: 3ffk
TitleCrystal structure of human Gelsolin domains G1-G3 bound to Actin
Components
  • actin, alpha skeletal muscle
  • plasma gelsolin
KeywordsSTRUCTURAL PROTEIN / Gelsolin / Actin / Ca-dependent / Ca-activated / contractile protein
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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...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 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / sarcoplasm / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cytoskeletal motor activator activity / phagocytosis, engulfment / cortical actin cytoskeleton / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / hepatocyte apoptotic process / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / cilium assembly / actin monomer binding / Caspase-mediated cleavage of cytoskeletal proteins / skeletal muscle fiber development / phagocytic vesicle / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / filopodium / central nervous system development / actin filament organization / 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 / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / cell body / actin binding / blood microparticle / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / hydrolase activity / Amyloid fiber formation / protein domain specific binding / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein 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)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsChumnarnsilpa, S. / Robinson, R.C. / Burtnick, L.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Ca2+ binding by domain 2 plays a critical role in the activation and stabilization of gelsolin.
Authors: Nag, S. / Ma, Q. / Wang, H. / Chumnarnsilpa, S. / Lee, W.L. / Larsson, M. / Kannan, B. / Hernandez-Valladares, M. / Burtnick, L.D. / Robinson, R.C.
History
DepositionDec 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: plasma gelsolin
B: actin, alpha skeletal muscle
D: plasma gelsolin
E: actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,48316
Polymers168,0684
Non-polymers1,41512
Water8,521473
1
A: plasma gelsolin
B: actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7428
Polymers84,0342
Non-polymers7086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-74 kcal/mol
Surface area30870 Å2
MethodPISA
2
D: plasma gelsolin
E: actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7428
Polymers84,0342
Non-polymers7086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-72 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.179, 146.923, 148.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein plasma gelsolin / actin-depolymerizing factor / ADF / Brevin / AGEL


Mass: 41937.105 Da / Num. of mol.: 2 / Fragment: UNP residues 52-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Plasmid: PSY5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STAR / References: UniProt: P06396
#2: Protein actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 42096.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: gene name ACTA1, ACTA / Source: (natural) Oryctolagus cuniculus (rabbit) / Organ: muscleSkeletal muscle / References: UniProt: P68135
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 18.015 Da / Num. of mol.: 473 / 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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 9% PEG 4000, 100 mM Sodium Acetate, 100 mM Calcium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 4.1 % / Av σ(I) over netI: 13.57 / Number: 184997 / Rmerge(I) obs: 0.097 / Χ2: 1.05 / D res high: 3 Å / D res low: 50 Å / Num. obs: 44802 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465098.810.0280.9844
5.136.4699.610.071.0154
4.485.1310010.0661.074.1
4.074.4899.910.0651.0294.2
3.784.0799.510.1021.0954.1
3.563.7899.710.1321.084.1
3.383.5699.710.181.1314.2
3.233.3899.910.2161.0724.2
3.113.2399.910.3061.0594.2
33.1197.710.3930.9684.2
ReflectionResolution: 2.998→50 Å / Num. obs: 44802 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.565
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.998-3.114.20.393197.7
3.11-3.234.20.306199.9
3.23-3.384.20.216199.9
3.38-3.564.20.18199.7
3.56-3.784.10.132199.7
3.78-4.074.10.102199.5
4.07-4.484.20.065199.9
4.48-5.134.10.0661100
5.13-6.4640.07199.6
6.46-5040.028198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.507 / Cor.coef. Fo:Fc: 0.471 / Cor.coef. Io to Ic: 0.525
Highest resolutionLowest resolution
Rotation3 Å15 Å
Translation3 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.845 / Occupancy max: 1 / Occupancy min: 1 / SU B: 26.07 / SU ML: 0.315 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27309 2264 5 %RANDOM
Rwork0.20088 ---
obs0.20448 42953 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.643 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11084 0 72 473 11629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.96315514
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84151419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87624.31529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.881151964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2881570
X-RAY DIFFRACTIONr_chiral_restr0.0840.21682
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218706
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.24906
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.27478
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2366
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1490.220
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4171.57037
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.797211344
X-RAY DIFFRACTIONr_scbond_it0.99334411
X-RAY DIFFRACTIONr_scangle_it1.7784.54166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 149 -
Rwork0.273 3119 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7505-0.2915-0.05921.33230.95843.4778-0.08890.07370.1399-0.01230.14850.0976-0.05510.0095-0.05960.0125-0.0143-0.02070.03840.04310.0548-12.17597.0463-33.2537
21.34330.29020.26593.00170.25651.2912-0.0428-0.06210.1108-0.1028-0.05720.209-0.0615-0.14060.10.00610.0081-0.01190.0164-0.01460.0243-44.692157.6859-23.4847
31.40060.3724-0.45120.62050.06591.03730.1297-0.1947-0.10420.1386-0.0599-0.11270.11840.195-0.06990.05220.0014-0.03780.04990.00360.0281-14.0502-2.8921-8.5955
40.4553-0.4552-0.43950.6875-0.14252.26520.04830.08940.12370.0551-0.0895-0.202-0.4631-0.19850.04120.10140.0437-0.01470.03720.02620.0616-44.639353.253-28.6235
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E28 - 370
2X-RAY DIFFRACTION2B6 - 365
3X-RAY DIFFRACTION3D27 - 365
4X-RAY DIFFRACTION4A756 - 759
5X-RAY DIFFRACTION4B380 - 401

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