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- PDB-6nbw: Ternary Complex of Beta/Gamma-Actin with Profilin and AnCoA-NAA80 -

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Basic information

Entry
Database: PDB / ID: 6nbw
TitleTernary Complex of Beta/Gamma-Actin with Profilin and AnCoA-NAA80
Components
  • Actin, cytoplasmic 1
  • 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 / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of actin polymerization or depolymerization / synapse maturation / peptide alpha-N-acetyltransferase activity / acetyl-CoA binding / modification of postsynaptic actin cytoskeleton ...N-terminal peptidyl-aspartic acid acetylation / N-terminal peptidyl-glutamic acid acetylation / actin modification / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of actin polymerization or depolymerization / synapse maturation / peptide alpha-N-acetyltransferase activity / acetyl-CoA binding / modification of postsynaptic actin cytoskeleton / regulation of transepithelial transport / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / morphogenesis of a polarized epithelium / bBAF complex / npBAF complex / brahma complex / postsynaptic actin cytoskeleton organization / nBAF complex / protein localization to adherens junction / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of G0 to G1 transition / dense body / Formation of annular gap junctions / Gap junction degradation / Signaling by ROBO receptors / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of actin filament polymerization / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / N-acetyltransferase activity / tight junction / positive regulation of ATP-dependent activity / PCP/CE pathway / regulation of norepinephrine uptake / proline-rich region binding / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of ruffle assembly / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / negative regulation of stress fiber assembly / apical junction complex / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / regulation of cyclin-dependent protein serine/threonine kinase activity / maintenance of blood-brain barrier / cortical cytoskeleton / positive regulation of actin filament polymerization / positive regulation of stem cell population maintenance / protein acetylation / nitric-oxide synthase binding / positive regulation of epithelial cell migration / Recycling pathway of L1 / kinesin binding / regulation of G1/S transition of mitotic cell cycle / brush border / calyx of Held / negative regulation of cell differentiation / positive regulation of double-strand break repair via homologous recombination / actin monomer binding / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / phosphatidylinositol-4,5-bisphosphate binding / EPHB-mediated forward signaling / substantia nigra development / phosphotyrosine residue binding / axonogenesis / negative regulation of protein binding / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / regulation of transmembrane transporter activity / adherens junction / FCGR3A-mediated phagocytosis / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
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 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Beta-Lactamase / Actin / Actin family / Actin / Acyl-CoA N-acyltransferase / ATPase, nucleotide binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / Chem-SOP / Profilin-1 / Actin, cytoplasmic 1 / N-alpha-acetyltransferase 80
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 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 1.2Mar 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, cytoplasmic 1
N: N-alpha-acetyltransferase 80
P: Profilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,80510
Polymers82,6593
Non-polymers2,1467
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-55 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.406, 115.594, 132.195
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, cytoplasmic 1 / Beta-actin


Mass: 41664.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60709
#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, 211 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 / Comment: toxin*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-SOP / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE / S-(2-OXOPROPYL)-COENZYME A


Mass: 823.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N7O17P3S
#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.: 204 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% PEG 3350, 50mM MES pH6.2, 50mM 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: 2.496→50 Å / Num. obs: 28132 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 21
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 4 / Num. unique obs: 2785 / % 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: 2.5→26.1 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 1399 5 %
Rwork0.1779 26573 -
obs0.1794 27972 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.16 Å2 / Biso mean: 43.413 Å2 / Biso min: 24.15 Å2
Refinement stepCycle: final / Resolution: 2.5→26.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5246 0 240 204 5690
Biso mean--36.13 36.79 -
Num. residues----672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.590.28021370.22682599273698
2.59-2.690.27911390.219726492788100
2.69-2.810.24461380.213326172755100
2.81-2.960.25631390.20526482787100
2.96-3.140.23491390.196926452784100
3.14-3.390.21481410.181626802821100
3.39-3.730.20291410.172326652806100
3.73-4.260.17261400.152926692809100
4.26-5.360.17011420.143326882830100
5.36-26.10.19781430.1812713285696

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