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- PDB-7ccc: The structure of the actin filament uncapping complex mediated by... -

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Basic information

Entry
Database: PDB / ID: 7ccc
TitleThe structure of the actin filament uncapping complex mediated by twinfilin
Components
  • (F-actin-capping protein subunit ...) x 2
  • Actin, alpha skeletal muscle
  • Twinfilin-1
KeywordsSTRUCTURAL PROTEIN / actin filament regulator
Function / homology
Function and homology information


: / : / Advanced glycosylation endproduct receptor signaling / COPI-independent Golgi-to-ER retrograde traffic / negative regulation of filopodium assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / F-actin capping protein complex / WASH complex / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production ...: / : / Advanced glycosylation endproduct receptor signaling / COPI-independent Golgi-to-ER retrograde traffic / negative regulation of filopodium assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / F-actin capping protein complex / WASH complex / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / negative regulation of actin filament polymerization / barbed-end actin filament capping / cell junction assembly / actin filament depolymerization / MHC class II antigen presentation / regulation of lamellipodium assembly / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / cytoskeletal motor activator activity / myosin heavy chain binding / positive regulation of cardiac muscle hypertrophy / tropomyosin binding / cortical cytoskeleton / actin filament bundle / troponin I binding / filamentous actin / myofibril / mesenchyme migration / brush border / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / RHOBTB2 GTPase cycle / skeletal muscle fiber development / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / sarcomere / filopodium / actin filament / cell morphogenesis / positive regulation of neuron projection development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ruffle membrane / calcium-dependent protein binding / actin filament binding / cell-cell junction / actin cytoskeleton / lamellipodium / actin binding / actin cytoskeleton organization / cell body / hydrolase activity / cadherin binding / protein domain specific binding / focal adhesion / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
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 / Severin / Severin / 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
ADENOSINE-5'-DIPHOSPHATE / F-actin-capping protein subunit alpha-1 / Actin, alpha skeletal muscle / Twinfilin-1 / F-actin-capping protein subunit alpha / F-actin-capping protein subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsRobinson, R.C. / Mwangangi, D.M.
Funding support1items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0028/2018
CitationJournal: Sci Adv / Year: 2021
Title: The structure of the actin filament uncapping complex mediated by twinfilin.
Authors: Mwangangi, D.M. / Manser, E. / Robinson, R.C.
History
DepositionJun 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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

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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: Twinfilin-1
C: F-actin-capping protein subunit alpha
D: F-actin-capping protein subunit beta
E: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,1479
Polymers188,2125
Non-polymers9354
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23520 Å2
ΔGint-126 kcal/mol
Surface area63960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.759, 168.662, 176.989
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, 3 molecules AEB

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


Mass: 42109.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Twinfilin-1 / Protein A6 / Protein tyrosine kinase 9


Mass: 40341.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TWF1, PTK9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12792

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F-actin-capping protein subunit ... , 2 types, 2 molecules CD

#3: Protein F-actin-capping protein subunit alpha


Mass: 32980.703 Da / Num. of mol.: 1 / Mutation: I222V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Capza1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5RKN9, UniProt: P47753*PLUS
#4: Protein F-actin-capping protein subunit beta


Mass: 30669.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Capzb / Production host: Escherichia coli (E. coli) / References: UniProt: Q923G3

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Non-polymers , 3 types, 58 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Sequence detailsTHE GENEBANK ACCESSION NUMBER IS 24771896 FOR THE PROTEIN.

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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: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 12% PEG 8000, 10% glycerol, 500 mM potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 34562 / % possible obs: 95.7 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.061 / Rrim(I) all: 0.198 / Χ2: 0.852 / Net I/σ(I): 4.5 / Num. measured all: 403423
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.057.22.0820970.4950.7612.2240.4594.4
3.05-3.117.81.78520900.5210.6321.9010.4792.5
3.11-3.178.31.54421000.5560.5291.6380.48694.6
3.17-3.238.81.29221050.6730.4311.3670.51493.5
3.23-3.39.21.12521400.7550.3671.1880.52795.1
3.3-3.389.40.96521200.8280.3081.0170.55694.3
3.38-3.469.60.85521480.8410.2710.90.65196
3.46-3.559.70.90921280.8930.2870.9560.6893.6
3.55-3.669.50.71721490.8550.2290.7551.36296.2
3.66-3.789.50.50221400.8770.160.5291.60994.4
3.78-3.919.80.35821340.9510.1130.3770.85694.7
3.91-4.069.70.30521500.9710.0960.3210.91395.2
4.06-4.259.80.20321310.9840.0640.2130.92693.8
4.25-4.479.60.16321690.9860.0520.1721.02694.7
4.47-4.759.40.13522050.990.0440.1421.01896.9
4.75-5.119.40.1322370.9920.0420.1371.01997.3
5.11-5.619.50.12722540.990.0410.1330.97698.3
5.61-6.49.60.11122950.9920.0360.1170.86698.8
6.4-7.989.60.08523390.9950.0280.090.86999.5
7.98-209.60.06724280.9970.0210.070.91799.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAW, 3AA7

3daw

3aa7


Resolution: 3.2→19.92 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 3431 9.93 %
Rwork0.1864 31131 -
obs0.1916 34558 91.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.22 Å2 / Biso mean: 55.7863 Å2 / Biso min: 9.29 Å2
Refinement stepCycle: final / Resolution: 3.2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12516 0 56 54 12626
Biso mean--34.09 39.79 -
Num. residues----1574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.240.35131230.2582966108973
3.24-3.290.296970.2461061115879
3.29-3.340.30571260.25591074120082
3.34-3.390.28751070.241137124483
3.39-3.450.37891220.24141142126486
3.45-3.510.31381420.26341130127286
3.51-3.570.36481220.28051181130387
3.57-3.640.31231220.25311210133291
3.64-3.710.3681300.27831199132989
3.71-3.790.25671180.22891253137193
3.79-3.880.23961190.19151271139093
3.88-3.970.2461330.20371259139293
3.97-4.080.23371300.18881275140595
4.08-4.20.23661480.16181263141193
4.2-4.330.2081420.14631265140794
4.33-4.490.17561420.14861285142796
4.49-4.660.17731590.13781294145396
4.66-4.870.21021300.14321315144597
4.87-5.130.19631710.15091303147497
5.13-5.440.19121500.15571346149698
5.44-5.850.20741800.17961312149298
5.85-6.420.21621430.18191367151099
6.42-7.310.20921470.18351386153399
7.31-9.060.2021610.151913921553100
9.07-19.920.20671670.14841445161299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.394-0.03330.36210.3254-0.29761.85560.01010.0010.4264-0.32250.1698-0.46930.21671.09290.050.4385-0.12640.10320.54520.04190.508328.2964-8.2652-35.9821
20.05740.0446-0.02590.0306-0.00730.01810.5030.6421-0.2279-0.2248-0.0909-0.6470.24610.51320.00041.08390.03870.04011.02550.15760.756433.5907-12.0358-53.7814
30.13530.13840.00171.5124-1.08130.86390.10540.72920.1218-0.93220.0522-0.32560.210.58530.1230.3271-0.08020.1880.7325-0.09380.628632.364-17.1802-40.4018
40.2207-0.20520.12480.285-0.14930.72840.03550.2285-0.0324-0.0151-0.0687-0.64610.15990.7953-0.00840.21-0.03870.01890.516-0.01980.490226.2202-16.9757-28.937
51.0766-0.0640.051.55440.45522.2536-0.0110.24070.2335-0.26950.0862-0.0464-0.1937-0.23490.00130.1934-0.0051-0.01570.35680.06040.29214.627-14.6757-42.0026
60.61590.9738-0.3741.7599-0.39450.37830.2118-0.0998-0.64880.1053-0.2041-0.81620.44070.5812-0.12140.5085-0.1047-0.06440.7436-0.00050.561730.4672-14.0652-21.949
71.47080.3775-0.38781.822-0.34810.7060.2144-0.2851-0.3868-0.35630.1870.31890.4159-0.5250.02230.7081-0.3601-0.22380.06410.46520.2499-0.9804-53.0026-71.2424
80.9818-0.03610.4060.6498-0.17320.18790.2626-0.6564-0.14490.68890.2805-0.54390.4379-0.29470.00010.67560.052-0.09330.62210.01950.519818.3362-43.0737-53.4576
90.68770.35350.15230.57540.0721.7536-0.29870.2867-0.36390.17270.1038-0.2640.86610.8036-0.02350.5580.0116-0.05610.44850.06230.578119.8961-16.8178-6.9297
101.84760.40920.45571.55460.14552.3645-0.1862-0.27320.13930.06370.0558-0.0269-0.076-0.1021-0.00170.24570.0372-0.02890.14590.02040.27838.3844-10.5104-5.1256
110.3770.1294-0.36440.33610.110.5459-0.01610.05820.02670.00860.16060.12390.206-0.30790.00020.2717-0.0498-0.1130.35060.07750.47912.4465-16.9615-6.8202
120.45910.23870.4240.28580.06190.55120.00270.24980.0206-0.33550.20950.29040.4833-0.0137-0.03080.6416-0.1413-0.04291.06130.08370.9252-18.1227-40.0072-29.5524
130.402-0.07730.21550.244-0.18690.2349-0.1293-0.1688-0.2890.23710.15380.36020.3053-0.33-0.01440.3057-0.26580.22660.62880.08490.4675-8.7112-60.4419-16.7797
140.4746-0.17410.0930.2924-0.21840.4585-0.1311-0.8925-0.10710.34290.05520.30650.2411-0.099-0.00380.4872-0.04980.03920.59660.11810.3829.4339-61.1041-5.8782
150.0323-0.0117-0.0060.0239-0.03070.0470.29090.1095-1.21490.2475-0.4461-0.72330.7023-0.0645-0.00060.90940.1413-0.0510.93020.05790.892317.758-70.4489-1.2379
163.224-0.33750.78561.1326-0.59341.7583-0.0020.26440.0673-0.0713-0.0357-0.31860.19550.30470.0040.3289-0.0547-0.01370.29130.04110.143918.3501-55.615-21.8064
170.8602-0.10670.18540.80140.00070.4483-0.0045-0.2276-0.101-0.54210.25610.55780.1395-0.10580.05720.45-0.2375-0.27360.4970.13340.339-1.4487-34.0194-52.7083
180.14320.12240.17160.51510.08030.2751-0.13770.06340.0040.17490.06390.65770.3726-0.5026-0.00110.574-0.2993-0.05710.89180.15430.7883-16.9223-52.0183-35.5403
190.3658-0.0838-0.14060.3454-0.17450.53190.02440.2839-0.0567-0.42760.36620.68920.2728-0.76983.22540.4547-0.413-0.48461.06450.38710.7948-19.9463-42.5499-52.2448
201.86460.67120.58661.58610.04211.74730.23960.78760.1294-0.5474-0.37160.45470.0757-0.2280.00830.4817-0.126-0.05370.58150.13170.3386-6.6031-41.1979-41.1515
211.35950.5259-0.00151.26360.26051.9348-0.24970.28771.0927-0.0205-0.0545-0.2306-0.5266-0.4318-0.03880.2294-0.118-0.06490.360.16620.3936-2.2997-33.4779-38.2092
220.70610.1622-0.25210.35020.1170.41280.34870.24980.4822-0.5011-0.13310.515-0.0529-0.5530.00390.53340.06570.03390.4430.17260.49760.7751-15.84-86.8357
230.0859-0.1292-0.09810.20650.15710.1194-0.05630.51320.7676-0.19290.1818-0.1010.12150.05260.12280.87610.12870.3420.5730.37270.6176.98-6.5105-82.221
240.586-0.0147-0.00990.9696-0.39980.73430.20020.31270.64330.15780.25420.532-0.1647-0.71270.04910.33810.1040.09750.44050.22850.5299-2.4547-20.5588-77.6726
251.08440.1905-0.17882.2593-0.43651.30610.1778-0.06430.0777-0.0942-0.1389-0.4401-0.13470.10840.00110.31020.01570.09010.1851-0.01890.322923.2517-23.4586-77.3758
260.142-0.46170.29592.52230.11551.76470.12530.33380.2368-0.12990.11110.82440.044-0.5542-0.75150.4722-0.0328-0.1020.35820.27180.3842-2.5011-32.0135-81.8262
270.2484-0.32610.2881.48670.20420.6675-0.196-0.95470.12150.6344-0.445-0.19540.463-0.0839-0.1050.60460.00270.16231.55090.47711.1605-16.8294-22.2319-71.5186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 38 )A5 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 68 )A39 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 92 )A69 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 165 )A93 - 165
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 334 )A166 - 334
6X-RAY DIFFRACTION6chain 'A' and (resid 335 through 370 )A335 - 370
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 123 )B1 - 123
8X-RAY DIFFRACTION8chain 'B' and (resid 124 through 165 )B124 - 165
9X-RAY DIFFRACTION9chain 'B' and (resid 166 through 194 )B166 - 194
10X-RAY DIFFRACTION10chain 'B' and (resid 195 through 285 )B195 - 285
11X-RAY DIFFRACTION11chain 'B' and (resid 286 through 310 )B286 - 310
12X-RAY DIFFRACTION12chain 'B' and (resid 311 through 341 )B311 - 341
13X-RAY DIFFRACTION13chain 'C' and (resid 8 through 60 )C8 - 60
14X-RAY DIFFRACTION14chain 'C' and (resid 61 through 106 )C61 - 106
15X-RAY DIFFRACTION15chain 'C' and (resid 107 through 118 )C107 - 118
16X-RAY DIFFRACTION16chain 'C' and (resid 119 through 252 )C119 - 252
17X-RAY DIFFRACTION17chain 'C' and (resid 253 through 276 )C253 - 276
18X-RAY DIFFRACTION18chain 'D' and (resid 2 through 70 )D2 - 70
19X-RAY DIFFRACTION19chain 'D' and (resid 71 through 137 )D71 - 137
20X-RAY DIFFRACTION20chain 'D' and (resid 138 through 195 )D138 - 195
21X-RAY DIFFRACTION21chain 'D' and (resid 196 through 249 )D196 - 249
22X-RAY DIFFRACTION22chain 'E' and (resid 5 through 55 )E5 - 55
23X-RAY DIFFRACTION23chain 'E' and (resid 56 through 78 )E56 - 78
24X-RAY DIFFRACTION24chain 'E' and (resid 79 through 165 )E79 - 165
25X-RAY DIFFRACTION25chain 'E' and (resid 166 through 334 )E166 - 334
26X-RAY DIFFRACTION26chain 'E' and (resid 335 through 355 )E335 - 355
27X-RAY DIFFRACTION27chain 'E' and (resid 356 through 372 )E356 - 372

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