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- PDB-6yga: Crystal structure of the apo NatC complex -

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Basic information

Entry
Database: PDB / ID: 6yga
TitleCrystal structure of the apo NatC complex
Components(N-alpha-acetyltransferase ...) x 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 / peptide alpha-N-acetyltransferase activity / U6 snRNP / precatalytic spliceosome / U4/U6 x U5 tri-snRNP complex / macroautophagy / mRNA splicing, via spliceosome / regulation of protein localization / mRNA binding ...N-terminal methionine Nalpha-acetyltransferase NatC / NatC complex / peptide alpha-N-acetyltransferase activity / U6 snRNP / precatalytic spliceosome / U4/U6 x U5 tri-snRNP complex / macroautophagy / mRNA splicing, via spliceosome / regulation of protein localization / mRNA binding / nucleus / cytosol / cytoplasm
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 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily ...LSM domain containing 1 / -alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 30-like / Mak10 subunit, NatC N(alpha)-terminal acetyltransferase / 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
Similarity search - Domain/homology
IODIDE ION / DI(HYDROXYETHYL)ETHER / N-alpha-acetyltransferase 38, NatC auxiliary subunit / N-alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.397 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 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,66337
Polymers112,8313
Non-polymers2,83234
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14910 Å2
ΔGint-22 kcal/mol
Surface area41720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.124, 140.421, 166.409
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: 18934.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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: 85065.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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: 8831.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MAK31, NAA38, YCR020C-A, YCR20C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P23059

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Non-polymers , 5 types, 215 molecules

#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 50.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 14.5% PEG 4000, 150 mM ammonium iodide and 100 mM sodium citrate, pH 6.1
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: 0.9797 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: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.397→46.23 Å / Num. obs: 85056 / % possible obs: 99.5 % / Redundancy: 6.987 % / Biso Wilson estimate: 46.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.139 / Χ2: 1.793 / Net I/σ(I): 11.34
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
2.4-2.546.6251.2171.418960113771135240.6171.31998.2
2.54-2.727.2390.7682.419340612916129040.8140.82699.9
2.72-2.937.0270.4793.878506412113121050.9190.51799.9
2.93-3.216.8460.2866.397623311172111360.9660.30999.7
3.21-3.597.260.1512.147268110014100110.9920.162100
3.59-4.146.8410.08719.5760524888088470.9960.09499.6
4.14-5.067.2620.05828.5954434749774960.9980.063100
5.06-7.116.8940.06326.2639945582757940.9980.06899.4
7.11-46.236.9210.0441.7122418326932390.9990.04399.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.397→46.23 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.27
RfactorNum. reflection% reflection
Rfree0.2247 2216 4.92 %
Rwork0.1936 --
obs0.1951 45029 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.78 Å2 / Biso mean: 65.7087 Å2 / Biso min: 26.72 Å2
Refinement stepCycle: final / Resolution: 2.397→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7706 0 100 181 7987
Biso mean--72.19 51.63 -
Num. residues----953
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.397-2.44890.31191200.2993253697
2.4489-2.50580.26631500.2675261099
2.5058-2.56850.28821240.24862634100
2.5685-2.63790.28871310.2462654100
2.6379-2.71550.23241420.23082637100
2.7155-2.80320.24971360.232680100
2.8032-2.90330.24261460.24052639100
2.9033-3.01960.28581330.24062671100
3.0196-3.1570.26881640.2228262599
3.157-3.32340.21291410.21712665100
3.3234-3.53150.22821340.20052701100
3.5315-3.80410.1821220.17722697100
3.8041-4.18670.20591430.1656268099
4.1867-4.79190.19791230.14832776100
4.7919-6.03520.23441440.1751273399
6.0352-46.230.19521630.1722287599
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)
14.31881.13310.89344.9512-0.27142.8123-0.05010.3091-0.0585-0.95110.0668-0.00080.597-0.09490.02050.6084-0.0710.06210.3742-0.08360.419143.041-24.1284108.9335
22.3921-2.28030.72993.4524-2.01094.06160.01380.3003-0.2272-0.34810.07080.12650.1505-0.3056-0.0550.3849-0.06870.01660.4361-0.05110.407536.0689-11.2527119.3199
31.15430.19620.56551.9133-2.34843.2409-0.24320.4754-0.0408-0.7714-0.2694-0.39330.67390.46220.51051.01490.00440.19970.782-0.09410.535455.2532-8.409489.0111
41.5389-0.3106-0.18782.90660.04583.07360.00940.44150.2012-0.8414-0.02760.1478-0.1444-0.13870.02050.61610.0154-0.06680.56550.1550.42733.759520.012598.8677
51.07770.44820.05221.971-0.31731.45860.0114-0.05490.11180.1279-0.0481-0.1509-0.13160.0330.02810.21590.00460.00260.36310.00610.411440.043311.8657136.9044
64.65920.22281.19855.81315.11224.70820.2223-0.51290.96271.1966-0.349-0.5136-1.4560.69340.1291.3865-0.2585-0.04790.5739-0.02380.689939.031235.9111165.8973
70.93510.426-0.00543.11830.22370.91750.01570.01110.02530.1146-0.07180.23450.16-0.22450.05360.2827-0.01530.01110.4389-0.0060.329423.0501-2.363139.6056
83.3723-2.5766-0.75223.62270.48551.44010.17410.9707-0.1652-1.0131-0.4622-0.40620.50620.23140.29971.029-0.03260.28630.8216-0.02140.520257.0294-8.587889.1873
93.17912.4465-4.23443.798-3.82585.806-0.03412.0396-0.0077-0.9243-1.5272-1.42120.56972.55961.3211.35730.32410.38621.71710.45181.24971.3515-8.628685.4262
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 728 )B525 - 728
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 65 )C3 - 65
9X-RAY DIFFRACTION9chain 'C' and (resid 66 through 77 )C66 - 77

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