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- PDB-7yne: Crystal structure of fragmin domain-1 (1-160) in complex with G-f... -

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Basic information

Entry
Database: PDB / ID: 7yne
TitleCrystal structure of fragmin domain-1 (1-160) in complex with G-form 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 / actin polymerization or depolymerization / barbed-end actin filament capping / 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 / actin polymerization or depolymerization / barbed-end actin filament capping / 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'-DIPHOSPHATE / 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: 2.7 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
DepositionJul 30, 2022Deposition 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)244,08332
Polymers241,4548
Non-polymers2,62924
Water4,810267
1
A: Actin, alpha skeletal muscle
B: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,17311
Polymers60,3632
Non-polymers8109
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-67 kcal/mol
Surface area20800 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle
D: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0889
Polymers60,3632
Non-polymers7247
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-75 kcal/mol
Surface area20180 Å2
MethodPISA
3
E: Actin, alpha skeletal muscle
F: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9116
Polymers60,3632
Non-polymers5474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-60 kcal/mol
Surface area20300 Å2
MethodPISA
4
G: Actin, alpha skeletal muscle
H: Actin-binding protein fragmin P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9116
Polymers60,3632
Non-polymers5474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-59 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.898, 97.999, 420.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 27 or (resid 28...
21(chain C and (resid 6 through 27 or (resid 28...
31(chain E and (resid 6 through 35 or resid 68...
41(chain G and (resid 6 through 90 or (resid 91...
12(chain B and ((resid 22 through 29 and (name N...
22(chain D and ((resid 22 through 29 and (name N...
32(chain F and ((resid 22 through 29 and (name N...
42(chain H and (resid 22 through 30 or (resid 31...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRPROPRO(chain A and (resid 6 through 27 or (resid 28...AA6 - 278 - 29
121ARGARGALAALA(chain A and (resid 6 through 27 or (resid 28...AA28 - 2930 - 31
131THRTHRPHEPHE(chain A and (resid 6 through 27 or (resid 28...AA5 - 3757 - 377
141THRTHRPHEPHE(chain A and (resid 6 through 27 or (resid 28...AA5 - 3757 - 377
151THRTHRPHEPHE(chain A and (resid 6 through 27 or (resid 28...AA5 - 3757 - 377
161THRTHRPHEPHE(chain A and (resid 6 through 27 or (resid 28...AA5 - 3757 - 377
211THRTHRPROPRO(chain C and (resid 6 through 27 or (resid 28...CC6 - 278 - 29
221ARGARGALAALA(chain C and (resid 6 through 27 or (resid 28...CC28 - 2930 - 31
231THRTHRPHEPHE(chain C and (resid 6 through 27 or (resid 28...CC5 - 3757 - 377
241THRTHRPHEPHE(chain C and (resid 6 through 27 or (resid 28...CC5 - 3757 - 377
251THRTHRPHEPHE(chain C and (resid 6 through 27 or (resid 28...CC5 - 3757 - 377
261THRTHRPHEPHE(chain C and (resid 6 through 27 or (resid 28...CC5 - 3757 - 377
311THRTHRVALVAL(chain E and (resid 6 through 35 or resid 68...EE6 - 358 - 37
321LYSLYSTRPTRP(chain E and (resid 6 through 35 or resid 68...EE68 - 7970 - 81
331ASPASPASPASP(chain E and (resid 6 through 35 or resid 68...EE8082
341THRTHRGLUGLU(chain E and (resid 6 through 35 or resid 68...EE6 - 3648 - 366
351ASPASPASPASP(chain E and (resid 6 through 35 or resid 68...EE8183
361THRTHRGLUGLU(chain E and (resid 6 through 35 or resid 68...EE6 - 3648 - 366
411THRTHRPHEPHE(chain G and (resid 6 through 90 or (resid 91...GG6 - 908 - 92
421TYRTYRTYRTYR(chain G and (resid 6 through 90 or (resid 91...GG9193
431THRTHRSERSER(chain G and (resid 6 through 90 or (resid 91...GG5 - 3687 - 370
441THRTHRSERSER(chain G and (resid 6 through 90 or (resid 91...GG5 - 3687 - 370
451THRTHRSERSER(chain G and (resid 6 through 90 or (resid 91...GG5 - 3687 - 370
461THRTHRSERSER(chain G and (resid 6 through 90 or (resid 91...GG5 - 3687 - 370
112GLUGLUALAALA(chain B and ((resid 22 through 29 and (name N...BB22 - 2924 - 31
122THRTHRGLUGLU(chain B and ((resid 22 through 29 and (name N...BB19 - 16021 - 162
132THRTHRGLUGLU(chain B and ((resid 22 through 29 and (name N...BB19 - 16021 - 162
142THRTHRGLUGLU(chain B and ((resid 22 through 29 and (name N...BB19 - 16021 - 162
152THRTHRGLUGLU(chain B and ((resid 22 through 29 and (name N...BB19 - 16021 - 162
212GLUGLUALAALA(chain D and ((resid 22 through 29 and (name N...DD22 - 2924 - 31
222THRTHRGLUGLU(chain D and ((resid 22 through 29 and (name N...DD19 - 16021 - 162
232THRTHRGLUGLU(chain D and ((resid 22 through 29 and (name N...DD19 - 16021 - 162
242THRTHRGLUGLU(chain D and ((resid 22 through 29 and (name N...DD19 - 16021 - 162
252THRTHRGLUGLU(chain D and ((resid 22 through 29 and (name N...DD19 - 16021 - 162
312GLUGLUALAALA(chain F and ((resid 22 through 29 and (name N...FF22 - 2924 - 31
322THRTHRGLUGLU(chain F and ((resid 22 through 29 and (name N...FF19 - 16021 - 162
332THRTHRGLUGLU(chain F and ((resid 22 through 29 and (name N...FF19 - 16021 - 162
342THRTHRGLUGLU(chain F and ((resid 22 through 29 and (name N...FF19 - 16021 - 162
352THRTHRGLUGLU(chain F and ((resid 22 through 29 and (name N...FF19 - 16021 - 162
412GLUGLUSERSER(chain H and (resid 22 through 30 or (resid 31...HH22 - 3024 - 32
422GLNGLNGLNGLN(chain H and (resid 22 through 30 or (resid 31...HH3133
432GLUGLUGLUGLU(chain H and (resid 22 through 30 or (resid 31...HH22 - 16024 - 162
442GLUGLUGLUGLU(chain H and (resid 22 through 30 or (resid 31...HH22 - 16024 - 162
452GLUGLUGLUGLU(chain H and (resid 22 through 30 or (resid 31...HH22 - 16024 - 162
462GLUGLUGLUGLU(chain H and (resid 22 through 30 or (resid 31...HH22 - 16024 - 162

NCS ensembles :
ID
1
2

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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: 18253.432 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: the first two residues (GP) were derived from the expression tag
Source: (gene. exp.) Physarum polycephalum (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q94707

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Non-polymers , 7 types, 291 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, 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.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.43 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, pH 5.0, 0.1 M calcium acetate, and 12% PEG4000

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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: Mar 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.7→49.21 Å / Num. obs: 65917 / % possible obs: 99.9 % / Redundancy: 7.267 % / Biso Wilson estimate: 57 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.173 / Rrim(I) all: 0.186 / Χ2: 0.828 / Net I/σ(I): 9.89 / Num. measured all: 479002
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
2.7-2.877.3291.3851.327649010446104360.5181.48999.9
2.87-3.067.4080.8432.373115987098700.7680.906100
3.06-3.317.3970.4943.9967833917191700.9230.531100
3.31-3.627.3680.2767.2162716851285120.9710.296100
3.62-4.057.3160.161256944778377830.990.172100
4.05-4.677.2270.09818.2749496684968490.9950.106100
4.67-5.77.1360.09518.7442047589358920.9960.102100
5.7-8.016.910.07821.0331980463046280.9970.085100
8.01-49.216.6190.0532.8518381280227770.9960.05599.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
XDSMar 15, 2019data reduction
XSCALEMar 15, 2019data scaling
MOLREP11.5.02phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W52

7w52


Resolution: 2.7→49.21 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3078 3295 5 %
Rwork0.2734 62605 -
obs0.2751 65900 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 354.95 Å2 / Biso mean: 86.3885 Å2 / Biso min: 17.73 Å2
Refinement stepCycle: final / Resolution: 2.7→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14297 0 147 267 14711
Biso mean--65.48 47.66 -
Num. residues----1924
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5217X-RAY DIFFRACTION8.937TORSIONAL
12C5217X-RAY DIFFRACTION8.937TORSIONAL
13E5217X-RAY DIFFRACTION8.937TORSIONAL
14G5217X-RAY DIFFRACTION8.937TORSIONAL
21B2108X-RAY DIFFRACTION8.937TORSIONAL
22D2108X-RAY DIFFRACTION8.937TORSIONAL
23F2108X-RAY DIFFRACTION8.937TORSIONAL
24H2108X-RAY DIFFRACTION8.937TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.740.45231320.416525102642100
2.74-2.780.35681340.353925482682100
2.78-2.830.36191380.340626082746100
2.83-2.870.39491340.333325502684100
2.87-2.920.33431340.307825512685100
2.92-2.970.34021370.307626092746100
2.97-3.030.28571340.304125392673100
3.03-3.090.34671360.317825812717100
3.09-3.160.35571370.319826252762100
3.16-3.230.36251340.336425372671100
3.23-3.320.40261360.31525942730100
3.32-3.40.29851360.296725802716100
3.4-3.510.31971360.277525922728100
3.51-3.620.32771360.278225712707100
3.62-3.750.29071380.276726292767100
3.75-3.90.30391360.267925932729100
3.9-4.070.27841400.258326542794100
4.07-4.290.28251360.24725742710100
4.29-4.560.29351380.231726252763100
4.56-4.910.29441390.23826402779100
4.91-5.40.27121390.248626532792100
5.4-6.180.32411410.256626812822100
6.18-7.790.27671420.270626892831100
7.79-49.210.26991520.24762872302499
Refinement TLS params.Method: refined / Origin x: 1.3189 Å / Origin y: 55.1945 Å / Origin z: 49.1629 Å
111213212223313233
T0.3795 Å20.0316 Å20.0036 Å2-0.3103 Å2-0.0526 Å2--0.0405 Å2
L-0.0308 °20.162 °20.1195 °2-0.5426 °20.0645 °2--0.1291 °2
S-0.1603 Å °-0.1322 Å °-0.128 Å °0.5668 Å °0.0134 Å °0.2756 Å °0.0239 Å °0.003 Å °-0.3292 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 375
2X-RAY DIFFRACTION1allA380 - 382
3X-RAY DIFFRACTION1allB19 - 160
4X-RAY DIFFRACTION1allB400 - 401
5X-RAY DIFFRACTION1allC5 - 375
6X-RAY DIFFRACTION1allC380 - 382
7X-RAY DIFFRACTION1allD19 - 160
8X-RAY DIFFRACTION1allD400 - 401
9X-RAY DIFFRACTION1allE6 - 364
10X-RAY DIFFRACTION1allE380 - 382
11X-RAY DIFFRACTION1allF19 - 160
12X-RAY DIFFRACTION1allF400 - 401
13X-RAY DIFFRACTION1allG5 - 368
14X-RAY DIFFRACTION1allG380 - 382
15X-RAY DIFFRACTION1allH22 - 160
16X-RAY DIFFRACTION1allH400 - 401
17X-RAY DIFFRACTION1allI1 - 4
18X-RAY DIFFRACTION1allJ1 - 2
19X-RAY DIFFRACTION1allK1
20X-RAY DIFFRACTION1allL1
21X-RAY DIFFRACTION1allS1 - 326

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