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- PDB-7dsb: Crystal structure of actin capping protein in complex with V-1 an... -

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Basic information

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


positive regulation of macromolecule biosynthetic process / regulation of barbed-end actin filament capping / 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 ...positive regulation of macromolecule biosynthetic process / regulation of barbed-end actin filament capping / 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 / regulation of striated muscle tissue development / 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 / regulation of cell size / cortical cytoskeleton / myofibril / positive regulation of protein metabolic process / brush border / actin monomer binding / phosphatidylinositol-4,5-bisphosphate binding / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / filopodium / positive regulation of NF-kappaB transcription factor activity / Schaffer collateral - CA1 synapse / Z disc / cell morphogenesis / neuron differentiation / actin filament binding / cell-cell junction / lamellipodium / actin cytoskeleton / regulation of translation / actin cytoskeleton organization / positive regulation of cell growth / protein tyrosine kinase activity / postsynaptic density / protein-containing complex binding / perinuclear region of cytoplasm / ATP binding / nucleus / 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 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta isoforms 1 and 2 / Myotrophin / Twinfilin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.44 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: Myotrophin
D: Twinfilin-1


Theoretical massNumber of molelcules
Total (without water)77,1314
Polymers77,1314
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-49 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.280, 87.480, 120.920
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 Myotrophin / Protein V-1


Mass: 13324.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTPN / Production host: Escherichia coli (E. coli) / References: UniProt: P58546
#4: Protein/peptide Twinfilin-1 / Protein A6


Mass: 3331.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q91YR1
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% (w/v) PEG 3350, 5% (v/v) isopropanol, 0.1M HEPES-NaOH (pH = 7.5)

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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: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.44→45.84 Å / Num. obs: 28229 / % possible obs: 99.8 % / Redundancy: 6.009 % / Biso Wilson estimate: 50.147 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.107 / Χ2: 0.858 / Net I/σ(I): 15.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.44-2.595.9890.9312.0144550.7151.0299.4
2.59-2.776.090.5673.3242230.8710.621100
2.77-2.996.1150.3525.2539330.9540.385100
2.99-3.286.0990.1989.1836480.9830.217100
3.28-3.666.0880.10216.9333360.9950.111100
3.66-4.226.0230.0627.6729330.9980.066100
4.22-5.165.9530.03839.0225310.9990.042100
5.16-7.255.8660.04335.3719810.9990.04799.9
7.25-45.845.2650.02553.5711890.9990.02898.8

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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: 3aaa

3aaa


Resolution: 2.44→45.84 Å / SU ML: 0.3142 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 1412 5 %
Rwork0.2075 26807 -
obs0.2096 28219 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.25 Å2
Refinement stepCycle: LAST / Resolution: 2.44→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5057 0 0 94 5151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335178
X-RAY DIFFRACTIONf_angle_d0.56317016
X-RAY DIFFRACTIONf_chiral_restr0.0403769
X-RAY DIFFRACTIONf_plane_restr0.0034925
X-RAY DIFFRACTIONf_dihedral_angle_d20.0681924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.530.31911370.28492599X-RAY DIFFRACTION98.99
2.53-2.630.32751390.25772639X-RAY DIFFRACTION100
2.63-2.750.28731390.2492642X-RAY DIFFRACTION99.96
2.75-2.90.2921400.25262659X-RAY DIFFRACTION100
2.9-3.080.29271390.2412641X-RAY DIFFRACTION99.89
3.08-3.320.28291410.22952681X-RAY DIFFRACTION99.93
3.32-3.650.25781410.21532683X-RAY DIFFRACTION100
3.65-4.180.25091420.18962697X-RAY DIFFRACTION100
4.18-5.260.19341430.16672719X-RAY DIFFRACTION99.97
5.26-45.840.21571510.19132847X-RAY DIFFRACTION99.57

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