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- PDB-6ygd: Crystal structure of the NatC complex bound to Gag peptide and CoA -

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Basic information

Entry
Database: PDB / ID: 6ygd
TitleCrystal structure of the NatC complex bound to Gag peptide and CoA
Components
  • (N-alpha-acetyltransferase ...) x 3
  • Major capsid protein
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 / N-terminal protein amino acid acetylation / 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 ...N-terminal methionine Nalpha-acetyltransferase NatC / NatC complex / N-terminal protein amino acid acetylation / 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 / viral capsid / 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 / Major coat protein, L-A virus / L-A virus major coat protein superfamily / L-A virus, major coat protein / 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 / Major coat protein, L-A virus / L-A virus major coat protein superfamily / L-A virus, major coat protein / 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 / N-alpha-acetyltransferase 38, NatC auxiliary subunit / Major capsid protein / N-alpha-acetyltransferase 35, NatC auxiliary subunit / N-alpha-acetyltransferase 30
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae virus L-A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.752 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: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,50026
Polymers112,9414
Non-polymers2,56022
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14230 Å2
ΔGint-119 kcal/mol
Surface area40660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.136, 134.927, 165.740
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 Major capsid protein / Gag protein / Major coat protein


Mass: 1281.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae virus L-A / References: UniProt: P32503

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Non-polymers , 5 types, 115 molecules

#5: Chemical ChemComp-COA / COENZYME A / 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 / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 14.5% 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: 2.75→45.337 Å / Num. obs: 28788 / % possible obs: 99.5 % / Redundancy: 6.562 % / Biso Wilson estimate: 55.1 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.194 / Rrim(I) all: 0.211 / Χ2: 1.025 / Net I/σ(I): 9.33 / Num. measured all: 188898
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
2.75-2.926.6831.3421.3229791457044580.5981.45697.5
2.92-3.126.8210.8952.0829432431643150.7450.97100
3.12-3.376.6970.5623.4226982403240290.8750.6199.9
3.37-3.696.2060.3046.123230374437430.9610.333100
3.69-4.126.9110.18410.4923303337333720.9860.199100
4.12-4.756.6680.11316.120057301130080.9930.12399.9
4.75-5.86.1150.11115.6715716257425700.9930.12299.8
5.8-8.146.4990.08420.0613375206020580.9970.09299.9
8.14-45.3375.6780.03442.027012124812350.9990.03799

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.11 Å43.73 Å
Translation7.11 Å43.73 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: 2.752→45.337 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.12
RfactorNum. reflection% reflection
Rfree0.248 1428 4.96 %
Rwork0.2039 --
obs0.2061 28784 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.05 Å2 / Biso mean: 67.3916 Å2 / Biso min: 20.44 Å2
Refinement stepCycle: final / Resolution: 2.752→45.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7734 0 84 93 7911
Biso mean--77.74 44.35 -
Num. residues----956
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7523-2.85070.34781370.2947261296
2.8507-2.96480.30641420.26942685100
2.9648-3.09970.30941610.26262657100
3.0997-3.26310.29541500.24772718100
3.2631-3.46740.31051350.23042727100
3.4674-3.7350.23871240.20242743100
3.735-4.11070.24231360.17722739100
4.1107-4.7050.1961310.16022757100
4.705-5.92570.22971430.18442800100
5.9257-45.3370.2171690.19622918100
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)
14.4908-0.2087-0.24614.38150.31513.1055-0.02550.57820.2489-0.84850.06380.1117-0.31990.00540.01170.401-0.0763-0.0870.36750.07670.34115.267321.801924.9036
24.3132-2.6994-0.98746.41920.35991.7866-0.04680.18380.0932-0.2160.1002-0.22580.1440.2809-0.01190.2671-0.0185-0.06960.450.02820.2311.77969.455235.4854
32.1363-0.53740.67171.6474-0.36492.4212-0.25620.55070.1133-1.01340.03520.5673-0.0001-0.44630.22251.1888-0.2035-0.48240.8630.17660.8118-6.06316.03555.1416
41.6194-0.27430.17823.0710.05864.2418-0.10120.4049-0.1322-1.22620.1089-0.04470.4131-0.0229-0.00070.9176-0.11410.06730.5308-0.10740.450114.8917-22.567616.7098
50.74411.1074-0.05532.9055-0.10440.7636-0.03940.11950.0236-0.05550.10430.30350.1635-0.1173-0.08010.21640.0127-0.04170.3934-0.00560.34777.7761-12.910353.9448
65.48420.4664-0.80275.1725-2.49652.02750.4815-0.7157-0.36491.2263-0.47820.20470.2203-0.170.05210.8743-0.17520.01040.5696-0.06230.41819.4847-35.982683.4824
71.14230.5002-0.00623.6246-0.62420.88450.00820.05090.08740.0614-0.1295-0.2279-0.19320.18840.10480.2377-0.002-0.05120.3586-0.03380.218224.88591.831855.9012
83.2266-2.55621.18036.6646-0.78482.0694-0.04970.74080.252-1.4642-0.28660.66310.4289-0.29870.3671.3084-0.3104-0.4780.85470.06430.7862-7.36635.42035.4473
92.27822.2023-0.94323.385-0.06272.4237-0.22890.4875-0.52350.240.3902-0.12820.3661-1.4363-0.19961.3684-0.0391-0.89481.27680.02381.7203-20.65794.8295-0.4465
100.4588-0.79280.19362.91862.16624.1152-0.31981.5664-0.7442-0.44270.5864-0.2334-0.1240.1946-0.4520.6721-0.1552-0.03010.9396-0.13520.4835.02164.848324.4364
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 5 through 65 )C5 - 65
9X-RAY DIFFRACTION9chain 'C' and (resid 66 through 75 )C66 - 75
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 6)D1 - 6

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