[English] 日本語
Yorodumi
- PDB-7w52: Crystal structure of fragmin domain-1 (15-160) in complex with actin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7w52
TitleCrystal structure of fragmin domain-1 (15-160) in complex with actin
Components
  • Actin, alpha skeletal muscle
  • Actin-binding protein fragmin P
KeywordsCONTRACTILE PROTEIN / actin dynamics / fragmin / gelsolin / ATP hydrolysis
Function / homology
Function and homology information


Striated Muscle Contraction / actin polymerization or depolymerization / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton ...Striated Muscle Contraction / actin polymerization or depolymerization / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / actin cytoskeleton / hydrolase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. ...Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle / Actin-binding protein fragmin P
Similarity search - Component
Biological speciesPhysarum polycephalum (eukaryote)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
AuthorsTakeda, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K17708 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structures and mechanisms of actin ATP hydrolysis.
Authors: Kanematsu, Y. / Narita, A. / Oda, T. / Koike, R. / Ota, M. / Takano, Y. / Moritsugu, K. / Fujiwara, I. / Tanaka, K. / Komatsu, H. / Nagae, T. / Watanabe, N. / Iwasa, M. / Maeda, Y. / Takeda, S.
History
DepositionNov 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin-binding protein fragmin P
C: Actin, alpha skeletal muscle
D: Actin-binding protein fragmin P
E: Actin, alpha skeletal muscle
F: Actin-binding protein fragmin P
G: Actin, alpha skeletal muscle
H: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,87636
Polymers234,7908
Non-polymers3,08628
Water26,8061488
1
A: Actin, alpha skeletal muscle
B: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,58711
Polymers58,6982
Non-polymers8909
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-62 kcal/mol
Surface area21260 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle
D: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4699
Polymers58,6982
Non-polymers7727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-61 kcal/mol
Surface area20890 Å2
MethodPISA
3
E: Actin, alpha skeletal muscle
F: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4108
Polymers58,6982
Non-polymers7126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-60 kcal/mol
Surface area21250 Å2
MethodPISA
4
G: Actin, alpha skeletal muscle
H: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4108
Polymers58,6982
Non-polymers7126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-63 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.987, 96.260, 426.923
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139
#2: Protein
Actin-binding protein fragmin P


Mass: 16587.561 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: the first two residues (GP) were derived from expression tag
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94707

-
Non-polymers , 6 types, 1516 molecules

#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1488 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, pH 4.5, 0.1 M calcium acetate, and 7% PEG3350

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2→46.673 Å / Num. obs: 157109 / % possible obs: 98.2 % / Redundancy: 6.568 % / Biso Wilson estimate: 42.022 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.081 / Χ2: 1.074 / Net I/σ(I): 17.42 / Num. measured all: 1031833
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.126.6330.8512.0616390925510247120.6520.92296.9
2.12-2.276.6940.5343.5615670324020234080.870.57997.5
2.27-2.456.690.3185.8214710422428219880.9420.34498
2.45-2.686.6690.2029.0713572220696203520.9760.21998.3
2.68-36.6320.11715.5312319918822185770.9920.12698.7
3-3.466.5480.06427.4710774516618164540.9970.06999
3.46-4.236.3460.03943.488943914191140930.9990.04399.3
4.23-5.966.2470.0352.186944511181111170.9990.03399.4
5.96-46.6736.0190.02755.6738567656264080.9990.0397.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSMar 15, 2019data reduction
XSCALEMar 15, 2019data scaling
MOLREP11.5.02phasing
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P8Z

1p8z


Resolution: 2.001→46.673 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 7853 5 %
Rwork0.2095 149183 -
obs0.2113 157036 98.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.23 Å2 / Biso mean: 42.3089 Å2 / Biso min: 16.93 Å2
Refinement stepCycle: final / Resolution: 2.001→46.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15542 0 172 1488 17202
Biso mean--34.1 46.3 -
Num. residues----1967
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.001-2.02330.37442470.3502467994
2.0233-2.04710.34582580.3112490097
2.0471-2.07210.29272550.2883485597
2.0721-2.09830.30972570.2833487697
2.0983-2.12590.32122550.2847485597
2.1259-2.15510.32652570.2776487397
2.1551-2.18590.32632600.26494298
2.1859-2.21850.29982550.2582484498
2.2185-2.25310.36112560.3314486197
2.2531-2.29010.33472600.2739494097
2.2901-2.32960.2932560.2296487598
2.3296-2.37190.26242620.2296496698
2.3719-2.41750.28442560.2367487298
2.4175-2.46690.29572620.236498398
2.4669-2.52050.32590.2264490498
2.5205-2.57920.26092610.2196497298
2.5792-2.64370.28552590.2204491698
2.6437-2.71510.26552660.218505199
2.7151-2.7950.26952590.2144492499
2.795-2.88520.28922640.2135501099
2.8852-2.98830.23282640.2141501299
2.9883-3.10790.25892650.2113503599
3.1079-3.24940.25642610.2153496299
3.2494-3.42060.26042660.2022505899
3.4206-3.63490.23022680.1937508599
3.6349-3.91540.21182660.1859506899
3.9154-4.30910.20732690.1717511599
4.3091-4.93210.1742710.1603513399
4.9321-6.21160.20912760.18845254100
6.2116-46.6730.22442830.2013536398

+
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