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- PDB-7w52: Crystal structure of fragmin domain-1 (15-160) in complex with actin -

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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 filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / phosphatidylinositol-4,5-bisphosphate binding / actin filament ...Striated Muscle Contraction / actin filament severing / barbed-end actin filament capping / actin polymerization or depolymerization / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / phosphatidylinositol-4,5-bisphosphate binding / 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 / 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. ...Villin/Gelsolin / Gelsolin homology domain / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

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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

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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

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Details

Has ligand of interestY

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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: 2.49 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

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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

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Phasing

PhasingMethod: molecular replacement

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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

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