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- PDB-7ank: Crystal structure of sarcomeric protein FATZ-1 (d91-FATZ-1 constr... -

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Basic information

Entry
Database: PDB / ID: 7ank
TitleCrystal structure of sarcomeric protein FATZ-1 (d91-FATZ-1 construct) in complex with half dimer of alpha-actinin-2
Components
  • (Alpha-actinin-2) x 2
  • Myozenin-1
KeywordsSTRUCTURAL PROTEIN / Z-disk complex / F-actin crosslinking protein / scaffolding protein / fuzzy complex
Function / homology
Function and homology information


negative regulation of skeletal muscle tissue regeneration / actin filament uncapping / FATZ binding / titin Z domain binding / phospholipase C-activating angiotensin-activated signaling pathway / skeletal muscle fiber adaptation / positive regulation of endocytic recycling / positive regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transporter activity / myofibril assembly ...negative regulation of skeletal muscle tissue regeneration / actin filament uncapping / FATZ binding / titin Z domain binding / phospholipase C-activating angiotensin-activated signaling pathway / skeletal muscle fiber adaptation / positive regulation of endocytic recycling / positive regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transporter activity / myofibril assembly / protein serine/threonine phosphatase inhibitor activity / telethonin binding / postsynaptic actin cytoskeleton / positive regulation of cation channel activity / negative regulation of protein localization to cell surface / LIM domain binding / microspike assembly / positive regulation of potassium ion transport / muscle cell development / focal adhesion assembly / Striated Muscle Contraction / Assembly and cell surface presentation of NMDA receptors / actinin binding / cardiac muscle cell development / Nephrin family interactions / negative regulation of calcineurin-NFAT signaling cascade / structural constituent of muscle / cortical actin cytoskeleton / sarcomere organization / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / pseudopodium / negative regulation of potassium ion transport / Long-term potentiation / postsynaptic density, intracellular component / skeletal muscle tissue development / titin binding / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Ras activation upon Ca2+ influx through NMDA receptor / nuclear receptor coactivator activity / platelet alpha granule lumen / molecular condensate scaffold activity / filopodium / cell projection / protein localization to plasma membrane / regulation of membrane potential / actin filament / postsynaptic density membrane / wound healing / Z disc / actin filament binding / actin cytoskeleton / integrin binding / Platelet degranulation / cell junction / actin binding / actin cytoskeleton organization / RAF/MAP kinase cascade / regulation of apoptotic process / transmembrane transporter binding / dendritic spine / cytoskeleton / cell adhesion / protein domain specific binding / focal adhesion / glutamatergic synapse / calcium ion binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / identical protein binding / nucleus / cytosol
Similarity search - Function
Myozenin / Calcineurin-binding protein (Calsarcin) / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. ...Myozenin / Calcineurin-binding protein (Calsarcin) / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Alpha-actinin-2 / Myozenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.204 Å
AuthorsSponga, A. / Arolas, J.L. / Rodriguez Chamorro, A. / Mlynek, G. / Hollerl, E. / Schreiner, C. / Pedron, M. / Kostan, J. / Ribeiro, E.A. / Djinovic-Carugo, K.
Funding support Austria, United Kingdom, 7items
OrganizationGrant numberCountry
European CommissionMarie Sklodowska-Curie Actions, ITN 238423
Austrian Science FundI525, I1593, P22276, P19060 and W1221 Austria
Christian Doppler ForschungsgesellschaftLaboratory for High-Content Structural Biology and Biotechnology Austria
Wellcome Trust201543/Z/16 United Kingdom
European CommissionAustrian-Slovak Interreg Project B301
Vienna Science and Technology Fund (WWTF)Chemical Biology project LS17-008 Austria
Research Platform Comammox Austria
CitationJournal: Sci Adv / Year: 2021
Title: Order from disorder in the sarcomere: FATZ forms a fuzzy but tight complex and phase-separated condensates with alpha-actinin.
Authors: Sponga, A. / Arolas, J.L. / Schwarz, T.C. / Jeffries, C.M. / Rodriguez Chamorro, A. / Kostan, J. / Ghisleni, A. / Drepper, F. / Polyansky, A. / De Almeida Ribeiro, E. / Pedron, M. / Zawadzka- ...Authors: Sponga, A. / Arolas, J.L. / Schwarz, T.C. / Jeffries, C.M. / Rodriguez Chamorro, A. / Kostan, J. / Ghisleni, A. / Drepper, F. / Polyansky, A. / De Almeida Ribeiro, E. / Pedron, M. / Zawadzka-Kazimierczuk, A. / Mlynek, G. / Peterbauer, T. / Doto, P. / Schreiner, C. / Hollerl, E. / Mateos, B. / Geist, L. / Faulkner, G. / Kozminski, W. / Svergun, D.I. / Warscheid, B. / Zagrovic, B. / Gautel, M. / Konrat, R. / Djinovic-Carugo, K.
History
DepositionOct 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-actinin-2
B: Alpha-actinin-2
C: Myozenin-1


Theoretical massNumber of molelcules
Total (without water)128,6953
Polymers128,6953
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SEC-SAXS experiment, cross-linking, cross-linking with mass spectrometry, isothermal titration calorimetry, N=1 (alpha-actinin-2 half dimer in the cell and FATZ-1 as titrant/ligand), ...Evidence: SAXS, SEC-SAXS experiment, cross-linking, cross-linking with mass spectrometry, isothermal titration calorimetry, N=1 (alpha-actinin-2 half dimer in the cell and FATZ-1 as titrant/ligand), light scattering, SEC-MALS experiment
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-35 kcal/mol
Surface area48840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.6, 56.92, 209.38
Angle α, β, γ (deg.)90, 94.56, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-actinin-2 / Alpha-actinin skeletal muscle isoform 2 / F-actin cross-linking protein


Mass: 62561.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN2 / Plasmid: modified pET-8 vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 (DE3) / References: UniProt: P35609
#2: Protein Alpha-actinin-2 / Alpha-actinin skeletal muscle isoform 2 / F-actin cross-linking protein


Mass: 44608.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN2 / Plasmid: modified pET-8 vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 (DE3) / References: UniProt: P35609
#3: Protein Myozenin-1 / Calsarcin-2 / Filamin- / actinin- and telethonin-binding protein / Protein FATZ


Mass: 21524.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: UNP Q9NP98 Sequence start 92 Sequence end 299 / Source: (gene. exp.) Homo sapiens (human) / Gene: MYOZ1, MYOZ / Plasmid: modified pET-46 vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 pLysS (DE3) / References: UniProt: Q9NP98

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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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Bis-Tris propane (pH 7.5), 100 mM sodium citrate, 10 mM zinc chloride, 12% w/w polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 3.2→46.9 Å / Num. obs: 26764 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 127.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Net I/σ(I): 14.1
Reflection shellResolution: 3.2→3.29 Å / Redundancy: 6 % / Rmerge(I) obs: 1.425 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1897 / CC1/2: 0.872 / % possible all: 93.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D1E

4d1e


Resolution: 3.204→46.94 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.462
RfactorNum. reflection% reflectionSelection details
Rfree0.2842 1288 -RANDOM
Rwork0.2548 ---
obs0.2562 26764 98.9 %-
Displacement parametersBiso mean: 206.61 Å2
Baniso -1Baniso -2Baniso -3
1-34.9199 Å20 Å243.9432 Å2
2---67.7215 Å20 Å2
3---32.8016 Å2
Refine analyzeLuzzati coordinate error obs: 0.68 Å
Refinement stepCycle: LAST / Resolution: 3.204→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7319 0 0 0 7319
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0077454HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8310049HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3608SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1287HARMONIC5
X-RAY DIFFRACTIONt_it7454HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion971SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5720SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion3.19
LS refinement shellResolution: 3.204→3.23 Å
RfactorNum. reflection% reflection
Rfree0.6311 30 -
Rwork0.4154 --
obs--83.67 %
Refinement TLS params.

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)
14.69612.53044.91235.11060.29398.20590.01070.1489-0.12750.14890.04710.0313-0.12750.0313-0.0579-0.1873-0.01030.29260.7843-0.1917-0.567445.1749-8.9517100.3116
22.16520.23441.09550.09361.01886.0029-0.0181-0.05410.2135-0.05410.019-0.00470.2135-0.0047-0.001-0.13640.03110.27210.48020.305-0.232633.9605-30.540794.937
33.2453-0.7975-1.57750-0.05621.7364-0.02140.06930.10310.06930.02090.01560.10310.01560.0005-0.00560.0279-0.19460.3018-0.0589-0.206117.7941-16.380867.6358
45.8295-0.02275.83711.89931.83398.2673-0.0555-0.23-0.4119-0.23-0.09430.3276-0.41190.32760.1498-0.26740.011-0.14310.4943-0.1495-0.2321-6.5513-9.473240.7884
53.2967-4.74527.71763.4514-5.053510.9829-0.0922-0.01120.134-0.01120.2682-0.27080.134-0.2708-0.1759-0.03180.0606-0.3776-0.2692-0.14230.1106-43.0101-4.7113-6.3386
66.9670.26427.18152.4999-0.22889.3042-0.0376-0.53330.1075-0.53330.1329-0.06790.1075-0.0679-0.0952-0.4096-0.1235-0.4651-0.14450.05580.2735-57.9354-21.4304-5.7622
75.50880.00662.99811.86311.720513.3363-0.01830.06040.14640.06040.0913-0.07790.1464-0.0779-0.073-0.64620.16410.13750.60470.0579-0.446-23.5772-17.803248.4688
8-0.11630.68140.62753.29951.22572.5352-0.0209-0.03080.0485-0.03080.01870.06340.04850.06340.00220.1857-0.08520.0390.18710.03160.0313-9.8663-0.131180.4359
99.5402-1.86762.13512.90810.546612.87780.0439-0.0550.2351-0.0550.00240.27990.23510.2799-0.0462-0.46250.3539-0.09710.7537-0.3763-0.494828.5637-10.173166.0641
100.4411-1.01940.48610.56242.15450.81490.00310.07880.01020.07880.0037-0.03490.0102-0.0349-0.00680.0131-0.0923-0.05740.0947-0.15960.0113-9.9089-0.562459.3716
111.6519-0.6259-4.52394.34642.24011.41760.00710.1471-0.06720.1471-0.0084-0.1258-0.0672-0.12580.0013-0.09820.0667-0.03410.0252-0.08610.1055-47.7006-9.984214.6267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|35 - 150}
2X-RAY DIFFRACTION2{A|151 - 257}
3X-RAY DIFFRACTION3{A|258 - 282}
4X-RAY DIFFRACTION4{A|283 - 385}
5X-RAY DIFFRACTION5{A|386 - 513}
6X-RAY DIFFRACTION6{B|506 - 627}
7X-RAY DIFFRACTION7{B|628 - 749}
8X-RAY DIFFRACTION8{B|750 - 826}
9X-RAY DIFFRACTION9{B|827 - 890}
10X-RAY DIFFRACTION10{C|183 - 198}
11X-RAY DIFFRACTION11{C|212 - 233}

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