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- PDB-7ds2: Crystal structure of actin capping protein in complex with twinfl... -

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Basic information

Entry
Database: PDB / ID: 7ds2
TitleCrystal structure of actin capping protein in complex with twinflin-1 C-terminus tail
Components
  • F-actin-capping protein subunit alpha-1
  • F-actin-capping protein subunit beta isoforms 1
  • Twinfilin-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 / 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 / negative regulation of filopodium assembly / sperm head-tail coupling apparatus ...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 / RHOBTB2 GTPase cycle / 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 polymerization or depolymerization / regulation of lamellipodium assembly / regulation of cell morphogenesis / lamellipodium assembly / positive regulation of cardiac muscle hypertrophy / cortical cytoskeleton / myofibril / brush border / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / filopodium / Schaffer collateral - CA1 synapse / Z disc / cell morphogenesis / actin filament binding / cell-cell junction / lamellipodium / actin cytoskeleton / actin cytoskeleton organization / protein tyrosine kinase activity / postsynaptic density / protein-containing complex binding / perinuclear region of cytoplasm / ATP binding / membrane / plasma membrane / 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-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / 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: Twinfilin-1


Theoretical massNumber of molelcules
Total (without water)64,8073
Polymers64,8073
Non-polymers00
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-45 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.040, 61.540, 161.470
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-1 / Protein A6


Mass: 4331.960 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Twf1, Ptk9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91YR1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 22.5% (w/v) PEG 400, 0.1M HEPES-NaOH (pH = 7.0)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→48.97 Å / Num. obs: 37412 / % possible obs: 96.5 % / Redundancy: 7.109 % / Biso Wilson estimate: 31.802 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.044 / Χ2: 0.971 / Net I/σ(I): 31.64
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-2.076.5080.2327.6954580.9680.25288.4
2.07-2.217.3040.15512.8555860.990.16696.7
2.21-2.397.3120.10618.2452580.9950.11496.9
2.39-2.617.2950.07724.1548890.9970.08297.6
2.61-2.927.2360.05333.544710.9990.05798.4
2.92-3.377.20.03547.1639880.9990.03898.9
3.37-4.127.170.02662.634250.9990.02899.3
4.12-5.817.0490.02370.22273310.02599.7
5.81-48.976.640.0269.78160410.02299.8

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
XDSdata processing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3aa7

3aa7


Resolution: 1.95→48.94 Å / SU ML: 0.1557 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.2733
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1835 1871 5 %
Rwork0.1666 35537 -
obs0.1675 37408 96.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.43 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4241 0 0 433 4674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00554537
X-RAY DIFFRACTIONf_angle_d0.73666180
X-RAY DIFFRACTIONf_chiral_restr0.0484672
X-RAY DIFFRACTIONf_plane_restr0.0042820
X-RAY DIFFRACTIONf_dihedral_angle_d21.6361759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.20911180.19582246X-RAY DIFFRACTION80.19
2-2.060.23721400.18472655X-RAY DIFFRACTION95.88
2.06-2.130.20041410.17352688X-RAY DIFFRACTION96.52
2.13-2.20.19611430.17232705X-RAY DIFFRACTION96.9
2.2-2.290.21541430.17482712X-RAY DIFFRACTION96.78
2.29-2.40.22721430.1752714X-RAY DIFFRACTION97.11
2.4-2.520.19871440.17722745X-RAY DIFFRACTION97.77
2.52-2.680.19831460.17732765X-RAY DIFFRACTION98.21
2.68-2.890.18831450.18072769X-RAY DIFFRACTION97.79
2.89-3.180.19621470.16932794X-RAY DIFFRACTION98.96
3.18-3.640.17161490.15762831X-RAY DIFFRACTION98.97
3.64-4.580.13781520.13642875X-RAY DIFFRACTION99.47
4.58-48.940.17841600.17453038X-RAY DIFFRACTION99.84

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