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- PDB-6ygb: Crystal structure of the NatC complex bound to CoA -

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Basic information

Entry
Database: PDB / ID: 6ygb
TitleCrystal structure of the NatC complex bound to CoA
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 / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / U6 snRNP / precatalytic spliceosome / U4/U6 x U5 tri-snRNP complex / macroautophagy / mRNA splicing, via spliceosome / regulation of protein localization ...N-terminal methionine Nalpha-acetyltransferase NatC / NatC complex / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid 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 / 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 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / Acetyltransferase (GNAT) family ...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. / Acetyltransferase (GNAT) family / LSM domain superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
COENZYME A / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.451 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,72933
Polymers111,6593
Non-polymers3,07030
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15110 Å2
ΔGint-87 kcal/mol
Surface area42180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.042, 139.789, 166.561
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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Non-polymers , 6 types, 220 molecules

#4: Chemical ChemComp-COA / COENZYME A


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


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-IOD / IODIDE ION


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


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 16.5% PEG 4000, 150 mM ammonium iodide and 100 mM sodium citrate, pH 6.3
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: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.45→45.434 Å / Num. obs: 42192 / % possible obs: 99.9 % / Redundancy: 6.611 % / Biso Wilson estimate: 47.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.161 / Χ2: 1.082 / Net I/σ(I): 10.85 / Num. measured all: 278939
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
2.45-2.66.7341.4441.2444871669766630.631.56599.5
2.6-2.786.340.9141.9340061632363190.7780.99799.9
2.78-36.9040.5773.2640779590959070.9030.624100
3-3.286.8510.3445.4437127542054190.9620.372100
3.28-3.676.3440.17110.2931504496849660.9890.186100
3.67-4.236.9230.09318.8830455439943990.9970.1100
4.23-5.176.5220.0626.7824511376037580.9980.06599.9
5.17-7.276.4190.06424.5119091297429740.9980.069100
7.27-45.4345.8980.0345.3710540180117870.9990.03399.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.17 Å45.43 Å
Translation7.17 Å45.43 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YGA

6yga


Resolution: 2.451→45.434 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.07
RfactorNum. reflection% reflection
Rfree0.2357 2090 4.96 %
Rwork0.2031 --
obs0.2047 42178 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.9 Å2 / Biso mean: 64.5389 Å2 / Biso min: 26.05 Å2
Refinement stepCycle: final / Resolution: 2.451→45.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7764 0 122 190 8076
Biso mean--78.39 50.22 -
Num. residues----961
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.451-2.50760.38371520.3479259999
2.5076-2.57030.33411190.30682617100
2.5703-2.63980.32361310.29242661100
2.6398-2.71750.27581440.26852623100
2.7175-2.80520.2641410.25082633100
2.8052-2.90540.27021430.25252616100
2.9054-3.02170.26521320.25272680100
3.0217-3.15920.30411650.23632600100
3.1592-3.32580.24671380.22822656100
3.3258-3.5340.22541300.20942691100
3.534-3.80680.21261210.18642673100
3.8068-4.18960.20571410.17092690100
4.1896-4.79530.18571240.15512742100
4.7953-6.03930.23441440.17982751100
6.0393-45.4340.21650.17092856100
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)
13.17481.06920.53464.2739-0.55282.4393-0.02470.1315-0.1114-0.77330.04390.15240.4787-0.1165-0.00470.5265-0.03580.02260.426-0.06970.411242.9244-24.1232108.9503
20.734-0.8773-0.7184.6876-0.60121.4026-0.03610.3885-0.1212-0.56580.14470.22680.2189-0.2876-0.11960.3302-0.0585-0.01510.479-0.03780.33736.0934-11.2151119.3467
31.08050.34920.19551.6333-2.08512.8472-0.22670.3026-0.0077-0.6949-0.1664-0.42810.35890.48670.3731.041-0.00630.19360.7975-0.08680.587855.0244-8.319589.1671
41.1673-0.22850.0242.43610.21822.40260.10780.46110.2782-0.8594-0.12770.0749-0.288-0.15510.03590.6810.1133-0.03720.65540.18490.463733.705220.165199.0873
50.65760.35930.13781.9692-0.06441.27030.04410.02310.13290.0577-0.0248-0.1554-0.15590.06-0.0190.2202-0.00790.02680.38540.02820.38640.312812.0451137.0176
62.161-0.00620.72673.81762.66875.46790.3985-0.65420.77410.8803-0.4582-0.3263-0.87910.54230.13771.0988-0.2277-0.00670.6721-0.03990.700139.120835.829166.3338
71.12790.4204-0.23412.99110.26050.76210.00070.03430.00110.1052-0.04960.24750.1339-0.15630.05940.2134-0.01290.00110.40420.01190.248523.0955-2.586139.5283
83.0677-1.495-0.3193.9689-0.39052.91130.09810.8391-0.1401-0.6659-0.4659-0.35920.24270.50290.36230.9249-0.01550.17490.77660.00380.529257.7192-8.893589.3288
98.0599-3.6802-2.16979.08810.61157.37140.08770.1527-0.0302-0.1268-0.756-1.5180.4161.36930.70641.00430.05030.1871.14340.15691.007771.5241-8.678885.8352
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 730 )B525 - 730
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 65 )C1 - 65
9X-RAY DIFFRACTION9chain 'C' and (resid 66 through 77 )C66 - 77

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