[English] 日本語
Yorodumi
- PDB-7ds4: Crystal structure of actin capping protein in complex with twinfl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ds4
TitleCrystal structure of actin capping protein in complex with twinflin-1 C-terminus tail F323K mutant
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)63,7893
Polymers63,7893
Non-polymers00
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-51 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.450, 66.720, 164.420
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

-
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: 3313.948 Da / Num. of mol.: 1 / Mutation: F323K / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q91YR1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5% (w/v) PEG 3350, 5% (v/v) ethanol, 50mM Tris-HCl (pH = 7.0)

-
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: Sep 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.85→44.22 Å / Num. obs: 50056 / % possible obs: 99.8 % / Redundancy: 6.353 % / Biso Wilson estimate: 36.274 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.068 / Χ2: 0.901 / Net I/σ(I): 17.73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.966.5050.6152.6379440.8740.66899.5
1.96-2.16.6020.3235.2575000.950.351100
2.1-2.266.4910.2128.3669870.9730.23199.9
2.26-2.486.4560.1412.3865030.9880.152100
2.48-2.776.2360.0842058780.9950.09299.8
2.77-3.26.0220.05629.1352020.9970.06199.8
3.2-3.916.0270.04535.8344620.9980.04999.8
3.91-5.516.330.03246.2235190.9990.03599.9
5.51-44.225.9920.0346.9620610.9990.03398.8

-
Phasing

PhasingMethod: molecular replacement

-
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: 1.85→44.22 Å / SU ML: 0.2838 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.3863
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2589 2502 5 %
Rwork0.2093 47549 -
obs0.2118 50051 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.75 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 0 421 4520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064240
X-RAY DIFFRACTIONf_angle_d0.84275762
X-RAY DIFFRACTIONf_chiral_restr0.0503632
X-RAY DIFFRACTIONf_plane_restr0.0045763
X-RAY DIFFRACTIONf_dihedral_angle_d23.36731579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.47171340.43192554X-RAY DIFFRACTION98.5
1.89-1.920.48591360.382588X-RAY DIFFRACTION99.89
1.92-1.970.35831380.30832617X-RAY DIFFRACTION100
1.97-2.010.31681380.26312610X-RAY DIFFRACTION99.96
2.01-2.060.31471370.24542606X-RAY DIFFRACTION99.93
2.06-2.120.32061380.24012624X-RAY DIFFRACTION99.93
2.12-2.180.32381380.24692629X-RAY DIFFRACTION100
2.18-2.250.39361370.27892599X-RAY DIFFRACTION99.93
2.25-2.330.34121370.25042607X-RAY DIFFRACTION100
2.33-2.420.26921400.2232652X-RAY DIFFRACTION99.96
2.42-2.530.26781380.21772623X-RAY DIFFRACTION99.89
2.53-2.670.29121390.22092639X-RAY DIFFRACTION99.86
2.67-2.830.25791390.21362637X-RAY DIFFRACTION99.68
2.84-3.050.26721390.21272658X-RAY DIFFRACTION99.71
3.05-3.360.2551410.19872660X-RAY DIFFRACTION99.79
3.36-3.850.2351400.18122679X-RAY DIFFRACTION99.82
3.85-4.850.1831440.15362724X-RAY DIFFRACTION99.9
4.85-44.220.18521490.18142843X-RAY DIFFRACTION99.2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more