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- PDB-7a8t: Crystal structure of sarcomeric protein FATZ-1 (mini-FATZ-1 const... -

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Basic information

Entry
Database: PDB / ID: 7a8t
TitleCrystal structure of sarcomeric protein FATZ-1 (mini-FATZ-1 construct) in complex with rod domain of alpha-actinin-2
Components
  • Alpha-actinin-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 / protein serine/threonine phosphatase inhibitor activity / positive 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 / protein serine/threonine phosphatase inhibitor activity / positive regulation of potassium ion transmembrane transporter activity / myofibril assembly / negative regulation of potassium ion transmembrane transporter activity / telethonin binding / positive regulation of cation channel activity / LIM domain binding / negative regulation of protein localization to cell surface / microspike assembly / postsynaptic actin cytoskeleton / muscle cell development / positive regulation of potassium ion transport / focal adhesion assembly / Striated Muscle Contraction / Assembly and cell surface presentation of NMDA receptors / cardiac muscle cell development / Nephrin family interactions / structural constituent of muscle / sarcomere organization / negative regulation of calcineurin-NFAT signaling cascade / cortical actin cytoskeleton / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / pseudopodium / postsynaptic density, intracellular component / negative regulation of potassium ion transport / Long-term potentiation / skeletal muscle tissue development / titin binding / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / regulation of membrane potential / Ras activation upon Ca2+ influx through NMDA receptor / nuclear receptor coactivator activity / platelet alpha granule lumen / filopodium / cell projection / actin filament / protein localization to plasma membrane / 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 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site ...Myozenin / Calcineurin-binding protein (Calsarcin) / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / 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: 2.69 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
University of Vienna Research Platform Comammox
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
DepositionAug 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,6712
Polymers66,6712
Non-polymers00
Water0
1
A: Alpha-actinin-2
B: Myozenin-1

A: Alpha-actinin-2
B: Myozenin-1


  • defined by author&software
  • Evidence: SAXS, SEC-SAXS experiment, cross-linking, cross-linking with mass spectrometry, isothermal titration calorimetry, N=2 (alpha-actinin-2 dimer in the cell and FATZ-1 as titrant/ligand), light ...Evidence: SAXS, SEC-SAXS experiment, cross-linking, cross-linking with mass spectrometry, isothermal titration calorimetry, N=2 (alpha-actinin-2 dimer in the cell and FATZ-1 as titrant/ligand), light scattering, SEC-MALS experiment
  • 133 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)133,3414
Polymers133,3414
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area14640 Å2
ΔGint-44 kcal/mol
Surface area55290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.440, 103.440, 218.143
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 56211.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN2 / Plasmid: modified pET3d vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 (DE3) / References: UniProt: P35609
#2: Protein Myozenin-1 / Calsarcin-2 / Filamin- / actinin- and telethonin-binding protein / Protein FATZ


Mass: 10459.210 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYOZ1, MYOZ / Plasmid: modified p3NH 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: 4.32 Å3/Da / Density % sol: 71.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES (pH 7.0), 16% w/v Jeffamine ED-2003

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.69→46.7 Å / Num. obs: 38093 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 80.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20
Reflection shellResolution: 2.69→2.77 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2640 / CC1/2: 0.915 / % possible all: 95.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HCI

1hci


Resolution: 2.69→46.58 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.242 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1862 4.89 %RANDOM
Rwork0.204 ---
obs0.205 38093 99.5 %-
Displacement parametersBiso max: 239.93 Å2 / Biso mean: 125.26 Å2 / Biso min: 78.83 Å2
Baniso -1Baniso -2Baniso -3
1--27.6946 Å20 Å20 Å2
2---27.6946 Å20 Å2
3---55.3893 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 2.69→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4309 0 0 0 4309
Num. residues----519
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2152SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes760HARMONIC5
X-RAY DIFFRACTIONt_it4386HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion567SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4930SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4386HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg5906HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.32
X-RAY DIFFRACTIONt_other_torsion3.49
LS refinement shellResolution: 2.69→2.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2553 30 3.94 %
Rwork0.2964 732 -
all0.2945 762 -
obs--88.89 %
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)
10.2860.0722-0.42190.6516-2.00774.3035-0.01820.0689-0.0697-0.1726-0.1809-0.05860.2908-0.3490.19910.553-0.0693-0.0264-0.3359-0.0916-0.157238.0833-7.2657-42.2112
23.3166-1.9149-3.2417-3.31662.84912.25220.03770.0582-0.1326-0.13210.03050.29670.15420.011-0.06820.42970.08640.1349-0.0456-0.0857-0.267225.236319.7104-140.548
31.1024-0.8162-1.0254-0.4797-0.05360.69520.067-0.1592-0.08860.04990.05260.47620.1927-0.33-0.11960.31790.1614-0.0342-0.05730.0228-0.138126.324519.2264-73.803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|273 - 746}A273 - 746
2X-RAY DIFFRACTION2{B|180 - 199}B180 - 199
3X-RAY DIFFRACTION3{B|216 - 240}B216 - 240

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