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- PDB-7ds8: Crystal structure of actin capping protein in complex with twinfl... -

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Basic information

Entry
Database: PDB / ID: 7ds8
TitleCrystal structure of actin capping protein in complex with twinflin-1/CD2AP CPI chimera peptide (CDN-TWC)
Components
  • CD2-associated protein,Twinfilin-1
  • F-actin-capping protein subunit alpha-1
  • F-actin-capping protein subunit beta isoforms 1
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 / response to glial cell derived neurotrophic factor / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / RHOBTB2 GTPase cycle / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / transforming growth factor beta1 production ...Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / response to glial cell derived neurotrophic factor / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / RHOBTB2 GTPase cycle / Factors involved in megakaryocyte development and platelet production / COPI-mediated anterograde transport / transforming growth factor beta1 production / localization of cell / negative regulation of filopodium assembly / negative regulation of small GTPase mediated signal transduction / slit diaphragm / Rab protein signal transduction / negative regulation of transforming growth factor beta1 production / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / response to transforming growth factor beta / podocyte differentiation / immunological synapse formation / endothelium development / nerve growth factor signaling pathway / protein heterooligomerization / negative regulation of actin filament polymerization / collateral sprouting / renal albumin absorption / substrate-dependent cell migration, cell extension / cell-cell adhesion mediated by cadherin / phosphatidylinositol 3-kinase regulatory subunit binding / cell junction assembly / barbed-end actin filament capping / filopodium assembly / membrane organization / actin polymerization or depolymerization / regulation of lamellipodium assembly / cell-cell junction organization / regulation of cell morphogenesis / Nephrin family interactions / podosome / lamellipodium assembly / clathrin binding / positive regulation of cardiac muscle hypertrophy / maintenance of blood-brain barrier / nuclear envelope lumen / neurotrophin TRK receptor signaling pathway / D-glucose import / cortical cytoskeleton / filamentous actin / myofibril / cell leading edge / brush border / protein secretion / actin monomer binding / adipose tissue development / lymph node development / stress-activated MAPK cascade / ruffle / ERK1 and ERK2 cascade / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / cytoskeleton organization / actin filament organization / hippocampal mossy fiber to CA3 synapse / trans-Golgi network membrane / positive regulation of protein secretion / regulation of actin cytoskeleton organization / filopodium / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein catabolic process / liver development / response to insulin / synapse organization / regulation of synaptic plasticity / SH3 domain binding / structural constituent of cytoskeleton / response to wounding / lipid metabolic process / positive regulation of protein localization to nucleus / response to virus / centriolar satellite / Schaffer collateral - CA1 synapse / male gonad development / fibrillar center / Z disc / cell morphogenesis / actin filament binding / cell-cell junction / late endosome / cell migration / T cell receptor signaling pathway / lamellipodium / actin cytoskeleton / growth cone / actin cytoskeleton organization / response to oxidative stress / protein-containing complex assembly / protein tyrosine kinase activity
Similarity search - Function
Twinfilin / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / 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 ...Twinfilin / CD2-associated protein, first SH3 domain / CD2-associated protein, second SH3 domain / CD2-associated protein, third SH3 domain / 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 / Variant SH3 domain / ADF-H/Gelsolin-like domain superfamily / SH3 domain / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta isoforms 1 and 2 / Twinfilin-1 / CD2-associated protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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: CD2-associated protein,Twinfilin-1


Theoretical massNumber of molelcules
Total (without water)63,5463
Polymers63,5463
Non-polymers00
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-52 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.690, 63.840, 144.970
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 CD2-associated protein,Twinfilin-1 / Adapter protein CMS / Cas ligand with multiple SH3 domains / Protein A6


Mass: 3070.646 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: twinflin-1/CD2AP CPI chimera peptide, residues 326-344 of twinfilin-1 (UNP Q91YR1, PKGPAGKRGIRRLIRGPAE) were N-terminally fused with residues 485-493 of CD2AP (UNP Q9Y5K6, NLLHLTANR)
Source: (synth.) Homo sapiens (human), (synth.) Mus musculus (house mouse)
References: UniProt: Q9Y5K6, UniProt: Q91YR1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 4% (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: Dec 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.95→48.325 Å / Num. obs: 41266 / % possible obs: 99.9 % / Redundancy: 7.165 % / Biso Wilson estimate: 31.271 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.116 / Χ2: 0.816 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-2.077.1080.7722.6165720.7750.83299.6
2.07-2.217.2530.5014.5261700.8950.54100
2.21-2.397.2590.3656.357890.9470.393100
2.39-2.617.2580.2518.9253080.9720.27100
2.61-2.927.2410.15313.0448490.990.165100
2.92-3.377.1970.08619.9843190.9960.093100
3.37-4.127.1230.04934.7536610.9990.053100
4.12-5.817.040.03148.4829000.9990.033100
5.81-48.3256.4610.0352.7416970.9990.03399

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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: 1.95→38.53 Å / SU ML: 0.2214 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.7589
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2328 2064 5 %
Rwork0.1867 39197 -
obs0.189 41261 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.68 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 0 0 408 4595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514318
X-RAY DIFFRACTIONf_angle_d0.7315863
X-RAY DIFFRACTIONf_chiral_restr0.049640
X-RAY DIFFRACTIONf_plane_restr0.0043776
X-RAY DIFFRACTIONf_dihedral_angle_d22.77941611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.33431360.26672576X-RAY DIFFRACTION99.12
1.99-2.040.25781350.22292567X-RAY DIFFRACTION99.96
2.04-2.10.29081330.2222534X-RAY DIFFRACTION99.96
2.1-2.160.23281360.19992585X-RAY DIFFRACTION100
2.16-2.230.25241370.18952601X-RAY DIFFRACTION99.96
2.23-2.310.22671370.19362588X-RAY DIFFRACTION100
2.31-2.40.26151350.19762580X-RAY DIFFRACTION99.96
2.4-2.510.30771370.20172592X-RAY DIFFRACTION99.96
2.51-2.640.25421370.20782617X-RAY DIFFRACTION100
2.64-2.810.26691370.2032590X-RAY DIFFRACTION99.96
2.81-3.030.26611380.19682623X-RAY DIFFRACTION99.96
3.03-3.330.2151380.18552631X-RAY DIFFRACTION100
3.33-3.810.20681390.16712643X-RAY DIFFRACTION100
3.81-4.80.19641410.14592673X-RAY DIFFRACTION100
4.8-38.530.19851480.18732797X-RAY DIFFRACTION99.53

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