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- PDB-7ds3: Crystal structure of actin capping protein in complex with twinfl... -

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Basic information

Entry
Database: PDB / ID: 7ds3
TitleCrystal structure of actin capping protein in complex with twinflin-2 C-terminus tail
Components
  • F-actin-capping protein subunit alpha-1
  • F-actin-capping protein subunit beta isoforms 1
  • Twinfilin-2
KeywordsCYTOSOLIC PROTEIN / actin dynamics / actin capping protein / twinfilin / CARMIL / V-1
Function / homology
Function and homology information


: / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / regulation of microvillus length / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / negative regulation of filopodium assembly ...: / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / regulation of microvillus length / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / negative regulation of filopodium assembly / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / negative regulation of actin filament polymerization / cell junction assembly / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cell projection organization / stereocilium / regulation of lamellipodium assembly / regulation of cell morphogenesis / lamellipodium assembly / cortical cytoskeleton / myofibril / brush border / actin monomer binding / positive regulation of axon extension / positive regulation of lamellipodium assembly / cellular response to retinoic acid / phosphatidylinositol-4,5-bisphosphate binding / cytoskeleton organization / protein kinase C binding / hippocampal mossy fiber to CA3 synapse / actin filament / filopodium / positive regulation of neuron projection development / cellular response to growth factor stimulus / Schaffer collateral - CA1 synapse / Z disc / cell morphogenesis / actin filament binding / lamellipodium / growth cone / actin cytoskeleton organization / postsynaptic density / intracellular signal transduction / perinuclear region of cytoplasm / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Twinfilin / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha ...Twinfilin / F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta isoforms 1 and 2 / Twinfilin-2
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å
AuthorsTakeda, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K17708 Japan
Japan Society for the Promotion of Science (JSPS)17K07373 Japan
Japan Society for the Promotion of Science (JSPS)20K06522 Japan
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural Insights into the Regulation of Actin Capping Protein by Twinfilin C-terminal Tail.
Authors: Takeda, S. / Koike, R. / Fujiwara, I. / Narita, A. / Miyata, M. / Ota, M. / Maeda, Y.
History
DepositionDec 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Apr 7, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-actin-capping protein subunit alpha-1
B: F-actin-capping protein subunit beta isoforms 1
C: Twinfilin-2


Theoretical massNumber of molelcules
Total (without water)63,7693
Polymers63,7693
Non-polymers00
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-47 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.510, 67.640, 164.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein F-actin-capping protein subunit alpha-1 / Beta-actinin subunit I / CapZ 36/32


Mass: 33001.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13127
#2: Protein F-actin-capping protein subunit beta isoforms 1 / Beta-actinin subunit II / CapZ 36/32 / CapZ B1 and B2


Mass: 27473.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CAPZB / Production host: Escherichia coli (E. coli) / References: UniProt: P14315
#3: Protein/peptide Twinfilin-2 / A6-related protein / mA6RP / Twinfilin-1-like protein


Mass: 3293.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9Z0P5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 5% (w/v) PEG 3350, 50mM Tris-HCl (pH = 7.0)

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.09→49.17 Å / Num. obs: 34883 / % possible obs: 99.9 % / Redundancy: 7.148 % / Biso Wilson estimate: 46.149 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.062 / Χ2: 0.87 / Net I/σ(I): 22.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.09-2.227.1330.6932.8455260.8340.74899.8
2.22-2.377.2790.4364.6652440.9410.47100
2.37-2.567.2970.2797.2148600.9750.301100
2.56-2.87.2820.16112.2345080.9910.173100
2.8-3.137.250.08521.4841000.9970.092100
3.13-3.627.1110.04637.1836330.9990.05100
3.62-4.427.0170.02956.2531140.9990.031100
4.42-6.236.9420.02367.45245810.025100
6.23-49.176.2350.02270.614400.9990.02498

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ds2

7ds2


Resolution: 2.09→49.17 Å / SU ML: 0.2581 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.9326
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251 1744 5 %
Rwork0.215 33133 -
obs0.2168 34877 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.49 Å2
Refinement stepCycle: LAST / Resolution: 2.09→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4130 0 0 239 4369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324241
X-RAY DIFFRACTIONf_angle_d0.54095749
X-RAY DIFFRACTIONf_chiral_restr0.0408624
X-RAY DIFFRACTIONf_plane_restr0.0028760
X-RAY DIFFRACTIONf_dihedral_angle_d21.8891579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.33851430.29772711X-RAY DIFFRACTION99.65
2.15-2.220.32841430.27032704X-RAY DIFFRACTION99.96
2.22-2.30.29691430.26132722X-RAY DIFFRACTION100
2.3-2.390.28671430.25442722X-RAY DIFFRACTION99.97
2.39-2.50.29821440.25422741X-RAY DIFFRACTION99.97
2.5-2.640.2861440.24762723X-RAY DIFFRACTION100
2.64-2.80.30311440.24242742X-RAY DIFFRACTION100
2.8-3.020.28221450.23572758X-RAY DIFFRACTION100
3.02-3.320.25321450.22022763X-RAY DIFFRACTION99.97
3.32-3.80.23921460.20452789X-RAY DIFFRACTION100
3.8-4.790.18781490.1782821X-RAY DIFFRACTION100
4.79-49.170.24621550.19672937X-RAY DIFFRACTION99.07
Refinement TLS params.Method: refined / Origin x: 5.57499558445 Å / Origin y: -17.2812431369 Å / Origin z: -19.7459615774 Å
111213212223313233
T0.238838143529 Å20.0798880637792 Å2-0.0293782520234 Å2-0.243912833025 Å2-0.0264416173567 Å2--0.279461278568 Å2
L0.691223505946 °20.388711002716 °20.0543163884431 °2-0.947491289413 °20.522160463302 °2--1.33221279989 °2
S0.0132573051565 Å °-0.0988201117557 Å °-0.0153252107318 Å °0.0919546537971 Å °-0.0187148611561 Å °-0.117654689655 Å °-0.030468297058 Å °0.0675866765218 Å °-1.0810169361E-5 Å °
Refinement TLS groupSelection details: all

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