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- PDB-6nas: Ternary Complex of Ac-Alpha-Actin with Profilin and AcCoA-NAA80 -

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Basic information

Entry
Database: PDB / ID: 6nas
TitleTernary Complex of Ac-Alpha-Actin with Profilin and AcCoA-NAA80
Components
  • Actin, alpha skeletal muscle
  • N-alpha-acetyltransferase 80
  • Profilin-1
KeywordsSTRUCTURAL PROTEIN/TRANSFERASE / acetylation / NAA80 / CYTOSOLIC PROTEIN / STRUCTURAL PROTEIN-TRANSFERASE complex
Function / homology
Function and homology information


N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / actin modification / regulation of actin polymerization or depolymerization / acetyl-CoA binding / synapse maturation / protein-N-terminal amino-acid acetyltransferase activity / adenyl-nucleotide exchange factor activity / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly ...N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / actin modification / regulation of actin polymerization or depolymerization / acetyl-CoA binding / synapse maturation / protein-N-terminal amino-acid acetyltransferase activity / adenyl-nucleotide exchange factor activity / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of actin filament polymerization / Signaling by ROBO receptors / N-acetyltransferase activity / positive regulation of ATP-dependent activity / proline-rich region binding / PCP/CE pathway / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / cytoskeletal motor activator activity / protein acetylation / myosin heavy chain binding / tropomyosin binding / actin filament bundle / positive regulation of actin filament polymerization / troponin I binding / filamentous actin / mesenchyme migration / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / positive regulation of epithelial cell migration / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / actin filament polymerization / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / neural tube closure / actin filament / filopodium / RHO GTPases Activate Formins / modulation of chemical synaptic transmission / small GTPase binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / Platelet degranulation / lamellipodium / cell body / actin binding / actin cytoskeleton organization / cell cortex / blood microparticle / cytoskeleton / hydrolase activity / protein stabilization / cadherin binding / protein domain specific binding / focal adhesion / calcium ion binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / glutamatergic synapse / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
N-alpha-acetyltransferase 80 / Profilin1/2/3, vertebrate / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic ...N-alpha-acetyltransferase 80 / Profilin1/2/3, vertebrate / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / Dynein light chain 2a, cytoplasmic / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Beta-Lactamase / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Acyl-CoA N-acyltransferase / Actin / Actin family / Actin / ATPase, nucleotide binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / Profilin-1 / Actin, alpha skeletal muscle / N-alpha-acetyltransferase 80
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRebowski, G. / Boczkowska, M. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073791 United States
CitationJournal: Sci Adv / Year: 2020
Title: Mechanism of actin N-terminal acetylation.
Authors: Rebowski, G. / Boczkowska, M. / Drazic, A. / Ree, R. / Goris, M. / Arnesen, T. / Dominguez, R.
History
DepositionDec 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
N: N-alpha-acetyltransferase 80
P: Profilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,13611
Polymers82,9123
Non-polymers2,2248
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-46 kcal/mol
Surface area28960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.830, 114.890, 132.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 3 types, 3 molecules ANP

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


Mass: 41917.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein N-alpha-acetyltransferase 80 / HsNAAA80 / N-acetyltransferase 6 / Protein fusion-2 / Protein fus-2


Mass: 25923.076 Da / Num. of mol.: 1 / Fragment: residues 56-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA80, FUS2, NAT6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q93015, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#3: Protein Profilin-1 / Epididymis tissue protein Li 184a / Profilin I


Mass: 15071.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07737

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Non-polymers , 7 types, 14 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO5S
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 16% Peg3350, 0.1 MES pH 6.5, 0.2M NH4NO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 2.899→50 Å / Num. obs: 17781 / % possible obs: 100 % / Redundancy: 39.4 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 24.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 40.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 1744 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PBD

2pbd


Resolution: 2.9→28.72 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 1772 10 %
Rwork0.184 15942 -
obs0.1894 17714 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.88 Å2 / Biso mean: 44.1477 Å2 / Biso min: 17.77 Å2
Refinement stepCycle: final / Resolution: 2.9→28.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5383 0 252 6 5641
Biso mean--36.41 29.47 -
Num. residues----688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.980.30331210.22171096121790
2.98-3.060.30091370.223112231360100
3.06-3.160.25881330.211931326100
3.16-3.280.32351360.207912341370100
3.28-3.410.24281370.202612251362100
3.41-3.560.24621360.198612261362100
3.56-3.750.26851360.179412231359100
3.75-3.980.21771370.178612351372100
3.98-4.290.21541370.161312351372100
4.29-4.720.18351380.146212351373100
4.72-5.40.20361380.167412461384100
5.4-6.790.24771410.200112721413100
6.79-28.720.2361450.18781299144498

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