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- PDB-7w4z: Crystal structure of fragmin domain-1 in complex with actin (AMPP... -

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Basic information

Entry
Database: PDB / ID: 7w4z
TitleCrystal structure of fragmin domain-1 in complex with actin (AMPPNP-form)
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 / stress fiber / skeletal muscle fiber development / 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 / stress fiber / skeletal muscle fiber development / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / 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: 1.15 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,35011
Polymers60,3632
Non-polymers9879
Water15,385854
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-54 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.090, 91.070, 114.850
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, 2 molecules AB

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


Mass: 42109.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P68139
#2: Protein Actin-binding protein fragmin P


Mass: 18253.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94707

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Non-polymers , 6 types, 863 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50 mM Na2HPO4, 19% 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: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.15→29.35 Å / Num. obs: 209417 / % possible obs: 98.7 % / Redundancy: 7.463 % / Biso Wilson estimate: 17.213 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.072 / Χ2: 0.929 / Net I/σ(I): 12.64 / Num. measured all: 1562876 / Scaling rejects: 351
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
1.15-1.186.391.0171.829502615568148710.6311.10695.5
1.18-1.216.9310.8542.2810227115183147560.7340.92297.2
1.21-1.256.9670.7312.6610024314726143890.7950.78997.7
1.25-1.297.0020.6173.169818214316140210.8480.66597.9
1.29-1.337.0460.5093.829626813937136630.8930.54998
1.33-1.377.0590.4254.589357813411132560.9220.45898.8
1.37-1.437.0950.3395.689092713007128160.9490.36598.5
1.43-1.487.1070.2647.18821212499124120.970.28599.3
1.48-1.557.1220.1979.218493212032119260.9820.21399.1
1.55-1.637.130.15711.198183011519114770.9890.16999.6
1.63-1.717.1650.12813.337802010929108890.9920.13799.6
1.71-1.827.1570.10315.87405710368103470.9940.11199.8
1.82-1.947.1470.08318.3169776977497630.9960.0999.9
1.94-2.17.0680.07121.8264488912891240.9960.077100
2.1-2.37.1370.06325.5960000840784070.9960.068100
2.3-2.577.370.05927.8156220762976280.9970.064100
2.57-2.9711.7620.05937.5779617676967690.9980.062100
2.97-3.6412.1190.0545.6569937577157710.9990.052100
3.64-5.1411.5240.04751.3552158452745260.9990.049100
5.14-29.3510.4120.04648.727134261426060.9980.04899.7

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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: 3j8a

3j8a


Resolution: 1.15→29.35 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1575 10471 5 %
Rwork0.1429 198941 -
obs0.1436 209412 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.64 Å2 / Biso mean: 19.5195 Å2 / Biso min: 8.25 Å2
Refinement stepCycle: final / Resolution: 1.15→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4073 0 56 878 5007
Biso mean--19.11 32.17 -
Num. residues----517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.160.27343280.26016234656294
1.16-1.180.23343400.23396462680297
1.18-1.190.22323400.22446465680597
1.19-1.210.2143400.20626456679698
1.21-1.220.20823440.20476533687798
1.22-1.240.18893410.1946485682697
1.24-1.260.20193420.1876489683198
1.26-1.280.17323440.17966543688798
1.28-1.30.18053440.17016533687798
1.3-1.320.1793440.16326542688699
1.32-1.340.17863460.1626574692098
1.34-1.360.15553460.14896568691498
1.36-1.390.16213460.14316577692399
1.39-1.420.14033500.13846634698499
1.42-1.450.13423460.13226576692299
1.45-1.480.14923480.12786628697699
1.48-1.520.15533500.11636632698299
1.52-1.560.13263500.1116652700299
1.56-1.610.14243510.11286670702199
1.61-1.660.15033530.109867047057100
1.66-1.720.14853520.117766917043100
1.72-1.790.15623530.125467137066100
1.79-1.870.1463500.132266557005100
1.87-1.970.15053570.129967787135100
1.97-2.090.14883540.133867357089100
2.09-2.250.14343580.129267917149100
2.25-2.480.15913570.140367947151100
2.48-2.840.16363590.150868177176100
2.84-3.570.16463630.150568987261100
3.57-29.350.14493750.140771127487100

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