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- PDB-6ygc: Crystal structure of the NatC complex bound to Arl3 peptide and CoA -

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Basic information

Entry
Database: PDB / ID: 6ygc
TitleCrystal structure of the NatC complex bound to Arl3 peptide and CoA
Components
  • (N-alpha-acetyltransferase ...) x 3
  • ADP-ribosylation factor-like protein 3
KeywordsTRANSFERASE / N-terminal acetylation / NAT / GNAT / acetyltransferase / Naa30 / Naa35 / Naa38 / Mak3 / Mak10 / Mak31
Function / homology
Function and homology information


N-terminal methionine Nalpha-acetyltransferase NatC / NatC complex / Retrograde transport at the Trans-Golgi-Network / N-terminal protein amino acid acetylation / protein localization to organelle / peptide alpha-N-acetyltransferase activity / U6 snRNP / protein localization to Golgi apparatus / Golgi to plasma membrane protein transport / nuclear outer membrane-endoplasmic reticulum membrane network ...N-terminal methionine Nalpha-acetyltransferase NatC / NatC complex / Retrograde transport at the Trans-Golgi-Network / N-terminal protein amino acid acetylation / protein localization to organelle / peptide alpha-N-acetyltransferase activity / U6 snRNP / protein localization to Golgi apparatus / Golgi to plasma membrane protein transport / nuclear outer membrane-endoplasmic reticulum membrane network / precatalytic spliceosome / U4/U6 x U5 tri-snRNP complex / response to endoplasmic reticulum stress / macroautophagy / intracellular protein transport / mRNA splicing, via spliceosome / regulation of protein localization / GTPase activity / mRNA binding / GTP binding / Golgi apparatus / nucleus / cytoplasm / cytosol
Similarity search - Function
LSM domain containing 1 / -alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 30-like / Mak10 subunit, NatC N(alpha)-terminal acetyltransferase / small GTPase Arf family profile. / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins ...LSM domain containing 1 / -alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 30-like / Mak10 subunit, NatC N(alpha)-terminal acetyltransferase / small GTPase Arf family profile. / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
COENZYME A / IODIDE ION / N-alpha-acetyltransferase 38, NatC auxiliary subunit / N-alpha-acetyltransferase 35, NatC auxiliary subunit / ADP-ribosylation factor-like protein 3 / N-alpha-acetyltransferase 30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.994 Å
AuthorsGrunwald, S. / Hopf, L. / Bock-Bierbaum, T. / Lally, C.C. / Spahn, C.M.T. / Daumke, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB958-A12 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Divergent architecture of the heterotrimeric NatC complex explains N-terminal acetylation of cognate substrates.
Authors: Grunwald, S. / Hopf, L.V.M. / Bock-Bierbaum, T. / Lally, C.C.M. / Spahn, C.M.T. / Daumke, O.
History
DepositionMar 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 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: N-alpha-acetyltransferase 30
B: N-alpha-acetyltransferase 35, NatC auxiliary subunit
C: N-alpha-acetyltransferase 38, NatC auxiliary subunit
D: ADP-ribosylation factor-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,28523
Polymers112,9214
Non-polymers2,36419
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-133 kcal/mol
Surface area41390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.303, 139.724, 166.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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N-alpha-acetyltransferase ... , 3 types, 3 molecules ABC

#1: Protein N-alpha-acetyltransferase 30 / L-A virus GAG protein N-acetyltransferase subunit MAK3 / Maintenance of killer protein 3 / N- ...L-A virus GAG protein N-acetyltransferase subunit MAK3 / Maintenance of killer protein 3 / N-terminal acetyltransferase C complex catalytic subunit MAK3 / NatC complex subunit MAK3 / NatC catalytic subunit


Mass: 18559.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAK3, NAA30, YPR051W, YP9499.08 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q03503, N-terminal methionine Nalpha-acetyltransferase NatC
#2: Protein N-alpha-acetyltransferase 35, NatC auxiliary subunit / Glucose repressible protein MAK10 / L-A virus GAG protein N-acetyltransferase subunit MAK10 / ...Glucose repressible protein MAK10 / L-A virus GAG protein N-acetyltransferase subunit MAK10 / Maintenance of killer protein 10 / N-terminal acetyltransferase C complex subunit MAK10 / NatC complex subunit MAK10


Mass: 84549.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAK10, NAA35, YEL053C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02197
#3: Protein N-alpha-acetyltransferase 38, NatC auxiliary subunit / L-A virus GAG protein N-acetyltransferase subunit MAK31 / Maintenance of killer protein 31 / N- ...L-A virus GAG protein N-acetyltransferase subunit MAK31 / Maintenance of killer protein 31 / N-terminal acetyltransferase C complex subunit MAK31 / NatC complex subunit MAK31


Mass: 8550.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAK31, NAA38, YCR020C-A, YCR20C-A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23059

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide ADP-ribosylation factor-like protein 3 / Arf-like GTPase 3


Mass: 1262.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02804

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Non-polymers , 5 types, 71 molecules

#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 16% PEG 4000, 150 mM ammonium iodide and 100 mM sodium citrate, pH 6.2
PH range: 6.1 - 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.99→46.397 Å / Num. obs: 23309 / % possible obs: 98.7 % / Redundancy: 4.036 % / Biso Wilson estimate: 57.24 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.166 / Rrim(I) all: 0.191 / Χ2: 0.984 / Net I/σ(I): 8.42 / Num. measured all: 94075
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.99-3.174.1450.8841.615200371636670.6241.01398.7
3.17-3.394.0590.552.5114251352535110.8140.63399.6
3.39-3.663.9730.3234.2312762328532120.930.37297.8
3.66-4.014.1680.1946.9612642304330330.9720.22399.7
4.01-4.484.0610.12910.0311183276427540.9870.14999.6
4.48-5.164.0410.0913.759722245724060.9930.10397.9
5.16-6.34.0240.10511.428423210720930.9910.1299.3
6.3-8.833.8410.06217.96323168416460.9970.07297.7
8.83-46.3973.6160.03133.21356910359870.9980.03795.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YGA

6yga


Resolution: 2.994→46.397 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.38
RfactorNum. reflection% reflection
Rfree0.2483 1156 4.96 %
Rwork0.1961 --
obs0.1986 23301 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.99 Å2 / Biso mean: 63.4532 Å2 / Biso min: 16.74 Å2
Refinement stepCycle: final / Resolution: 2.994→46.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7753 0 86 52 7891
Biso mean--67 39.78 -
Num. residues----957
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.994-3.12990.3471600.3055267198
3.1299-3.29480.26721540.26322732100
3.2948-3.50120.30351280.2394273498
3.5012-3.77140.23341270.1926276099
3.7714-4.15070.22151430.17422758100
4.1507-4.75080.19851310.1565276398
4.7508-5.98350.24971470.17862836100
5.9835-46.3970.24531660.1846289197
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)
15.17682.26521.17025.14560.61894.5506-0.06920.1613-0.1794-0.6981-0.00610.05540.5715-0.22930.07180.44990.02270.04470.4061-0.06960.419243.2351-24.0572109.1329
22.5768-1.72620.59999.2011-1.6893.3225-0.03320.2862-0.1576-0.41660.17810.1882-0.2513-0.0507-0.13340.2452-0.03040.02230.4998-0.05160.294436.5996-11.1344119.4196
31.11350.89081.13691.1975-2.41143.4957-0.28320.3163-0.2667-0.6445-0.1402-0.51430.4390.55490.23080.85560.12720.28920.7596-0.05880.593955.1866-8.148188.8786
42.7019-0.2933-0.40633.38851.32412.70850.15620.56660.3465-0.9552-0.23180.0174-0.5511-0.35160.11870.81720.2446-0.00550.69220.25090.442433.846620.347999.5294
51.41360.8911-0.19073.0173-0.18851.27530.1425-0.0630.18930.088-0.1424-0.189-0.19640.08220.0230.20630.01560.00350.4473-0.00730.374340.462111.8995137.3386
62.693-0.75271.02921.86022.58365.72850.9113-0.13370.64870.3429-0.8039-0.3897-1.2170.71040.10231.2951-0.29320.03140.598-0.0320.655539.410235.7247166.5287
70.93830.2421-0.2742.83280.4781.01540.0234-0.0334-0.01670.0634-0.08370.18050.121-0.29650.08390.22550.0042-0.00680.58810.00240.348223.3748-3.0065139.4467
84.4428-1.7472-0.07595.7849-1.55388.44660.35930.8767-0.2602-0.9048-0.3746-0.2733-0.2410.62720.12930.80740.01530.2340.7771-0.04540.513756.6501-8.069689.1639
92.3198-1.9784-0.27393.20821.45210.9316-0.18911.38940.1186-0.0604-0.2374-0.950.47931.16630.55121.11970.13180.51731.21160.27841.104271.5181-8.119285.5346
100.03330.01970.00020.0353-0.0110.00520.3511-0.05280.4607-0.11470.1473-0.24940.2372-0.0033-0.00051.25090.26920.06381.0946-0.18791.039142.6693-8.8431109.2396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 112 )A1 - 112
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 159 )A113 - 159
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 68 )B0 - 68
4X-RAY DIFFRACTION4chain 'B' and ((resid 69 through 309 ) or (resid 334 through 340))B0
5X-RAY DIFFRACTION5chain 'B' and ((resid 310 through 333 ) or (resid 341 through 493))B0
6X-RAY DIFFRACTION6chain 'B' and (resid 494 through 524 )B494 - 524
7X-RAY DIFFRACTION7chain 'B' and (resid 525 through 731 )B525 - 731
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 65 )C4 - 65
9X-RAY DIFFRACTION9chain 'C' and (resid 66 through 77 )C66 - 77
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 4 )D1 - 4

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