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- PDB-6swt: Affimer9 co-crystalised with the CH domains of alpha actinin 2. -

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Basic information

Entry
Database: PDB / ID: 6swt
TitleAffimer9 co-crystalised with the CH domains of alpha actinin 2.
Components
  • Affimer 9
  • Alpha-actinin-2
KeywordsCONTRACTILE PROTEIN / alpha-actinin 2 / Affimer
Function / homology
Function and homology information


actin filament uncapping / FATZ binding / titin Z domain binding / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / positive regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transporter activity / postsynaptic actin cytoskeleton / positive regulation of cation channel activity / negative regulation of protein localization to cell surface ...actin filament uncapping / FATZ binding / titin Z domain binding / phospholipase C-activating angiotensin-activated signaling pathway / positive regulation of endocytic recycling / positive regulation of potassium ion transmembrane transporter activity / negative regulation of potassium ion transmembrane transporter activity / 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 / cardiac muscle cell development / Nephrin family interactions / 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 / 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 / filopodium / cell projection / protein localization to plasma membrane / regulation of membrane potential / actin filament / postsynaptic density membrane / Z disc / actin filament binding / integrin binding / Platelet degranulation / cell junction / 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 / extracellular exosome / extracellular region / identical protein binding / cytosol
Similarity search - Function
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 ...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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsPeckham, M. / Trinh, C.H. / Rogers, B.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K015613/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M011151/1 United Kingdom
CitationJournal: Nano Lett. / Year: 2021
Title: Nanoscale Pattern Extraction from Relative Positions of Sparse 3D Localizations.
Authors: Curd, A.P. / Leng, J. / Hughes, R.E. / Cleasby, A.J. / Rogers, B. / Trinh, C.H. / Baird, M.A. / Takagi, Y. / Tiede, C. / Sieben, C. / Manley, S. / Schlichthaerle, T. / Jungmann, R. / Ries, J. ...Authors: Curd, A.P. / Leng, J. / Hughes, R.E. / Cleasby, A.J. / Rogers, B. / Trinh, C.H. / Baird, M.A. / Takagi, Y. / Tiede, C. / Sieben, C. / Manley, S. / Schlichthaerle, T. / Jungmann, R. / Ries, J. / Shroff, H. / Peckham, M.
History
DepositionSep 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-actinin-2
B: Affimer 9


Theoretical massNumber of molelcules
Total (without water)39,9732
Polymers39,9732
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-7 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.192, 48.519, 146.993
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29074.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN2 / Production host: Escherichia coli (E. coli) / References: UniProt: P35609
#2: Protein Affimer 9


Mass: 10898.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.2→73.5 Å / Num. obs: 103011 / % possible obs: 98.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 13.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Rrim(I) all: 0.079 / Net I/σ(I): 10.4
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7078 / CC1/2: 0.622 / Rpim(I) all: 0.493 / Rrim(I) all: 0.948 / % possible all: 93.3

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0257refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A38, 4N6T

5a38

4n6t


Resolution: 1.2→73.5 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.162 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.034
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.164 5321 5.2 %RANDOM
Rwork0.1491 ---
obs0.1499 97591 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.42 Å2 / Biso mean: 21.326 Å2 / Biso min: 9.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 1.2→73.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 0 230 2808
Biso mean---31.99 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132666
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172537
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.6373606
X-RAY DIFFRACTIONr_angle_other_deg1.4521.5825900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2885324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14923.022139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.72515505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.811514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022923
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02547
X-RAY DIFFRACTIONr_rigid_bond_restr1.06935203
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 319 -
Rwork0.254 6723 -
all-7042 -
obs--92.68 %

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