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- PDB-6nbe: Ternary Complex of Ac-Alpha-Actin with Profilin and CoA-NAA80 -

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Basic information

Entry
Database: PDB / ID: 6nbe
TitleTernary Complex of Ac-Alpha-Actin with Profilin and CoA-NAA80
Components
  • Actin, alpha skeletal muscle
  • N-alpha-acetyltransferase 80
  • Profilin-1
KeywordsSTRUCTURAL PROTEIN/TRANSFERASE / 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
ADENOSINE-5'-TRIPHOSPHATE / COENZYME A / 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 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 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Oct 11, 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
N: N-alpha-acetyltransferase 80
P: Profilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,09411
Polymers82,9123
Non-polymers2,1828
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9570 Å2
ΔGint-46 kcal/mol
Surface area29550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.469, 115.886, 132.488
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, 467 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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#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.: 459 / 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: 2.58 Å3/Da / Density % sol: 52.36 %
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→50 Å / Num. obs: 54090 / % possible obs: 100 % / Redundancy: 26.3 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 30.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 25.6 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 5172 / % 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→33.35 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.184 2000 3.7 %
Rwork0.159 52009 -
obs0.16 54009 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.12 Å2 / Biso mean: 36.62 Å2 / Biso min: 15.19 Å2
Refinement stepCycle: final / Resolution: 2→33.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5425 0 245 459 6129
Biso mean--33.24 38.14 -
Num. residues----694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.23861360.19133538367496
2.05-2.110.22721420.173536953837100
2.11-2.170.18661410.16736863827100
2.17-2.240.18911410.162736723813100
2.24-2.320.17181440.161437043848100
2.32-2.410.1971410.155936943835100
2.41-2.520.20851440.157537123856100
2.52-2.660.17571410.154736953836100
2.66-2.820.17781430.154537133856100
2.82-3.040.18931430.158437233866100
3.04-3.350.19361440.156737373881100
3.35-3.830.16861440.145137593903100
3.83-4.820.15391460.136537963942100
4.82-33.350.19951500.18833885403599

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