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- PDB-3tfy: Naa50p amino-terminal acetyltransferase bound to substrate peptid... -

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Basic information

Entry
Database: PDB / ID: 3tfy
TitleNaa50p amino-terminal acetyltransferase bound to substrate peptide fragment and CoA
Components
  • N-alpha-acetyltransferase 50, NatE catalytic subunit
  • hnRNP F
KeywordsTRANSFERASE / GNAT Family / N(alpha)-acetyltransferase
Function / homology
Function and homology information


: / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / FGFR2 alternative splicing / mitotic sister chromatid cohesion ...: / mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / FGFR2 alternative splicing / mitotic sister chromatid cohesion / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / single-stranded RNA binding / ribonucleoprotein complex / synapse / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Zinc finger, CHHC-type / RNPHF zinc finger / : / : / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase ...Zinc finger, CHHC-type / RNPHF zinc finger / : / : / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Heterogeneous nuclear ribonucleoprotein F / N-alpha-acetyltransferase 50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLiszczak, G.P. / Marmorstein, R.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of a Ternary Naa50p (NAT5/SAN) N-terminal Acetyltransferase Complex Reveals the Molecular Basis for Substrate-specific Acetylation.
Authors: Liszczak, G. / Arnesen, T. / Marmorstein, R.
History
DepositionAug 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-alpha-acetyltransferase 50, NatE catalytic subunit
D: hnRNP F
B: N-alpha-acetyltransferase 50, NatE catalytic subunit
E: hnRNP F
C: N-alpha-acetyltransferase 50, NatE catalytic subunit
F: hnRNP F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7659
Polymers61,4636
Non-polymers2,3033
Water1,67593
1
A: N-alpha-acetyltransferase 50, NatE catalytic subunit
D: hnRNP F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2553
Polymers20,4882
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-6 kcal/mol
Surface area8780 Å2
MethodPISA
2
B: N-alpha-acetyltransferase 50, NatE catalytic subunit
E: hnRNP F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2553
Polymers20,4882
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-6 kcal/mol
Surface area8470 Å2
MethodPISA
3
C: N-alpha-acetyltransferase 50, NatE catalytic subunit
F: hnRNP F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2553
Polymers20,4882
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-7 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.299, 104.103, 68.247
Angle α, β, γ (deg.)90.00, 106.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-alpha-acetyltransferase 50, NatE catalytic subunit / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog / hSAN


Mass: 19427.373 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAK3, NAA50, NAT13, NAT5 / Plasmid: pETM-GST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9GZZ1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide hnRNP F


Mass: 1060.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / References: UniProt: P52597*PLUS
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5
Details: well solution: 16% PEG 8000, 20% glycerol, 40mM potassium phosphate (monobasic), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2010 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 17043 / Num. obs: 16856 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 12.9 / Net I/σ(I): 10.2
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 682 / Rsym value: 40.9 / % possible all: 93.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PSW (cofactor and solvent removed)

2psw


Resolution: 2.75→33.659 Å / SU ML: 0.39 / σ(F): 0.19 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 813 5.08 %
Rwork0.1903 --
obs0.1935 16010 94.69 %
all-17043 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.837 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.8989 Å2-0 Å2-9.188 Å2
2---22.5298 Å20 Å2
3---0.6309 Å2
Refinement stepCycle: LAST / Resolution: 2.75→33.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3823 0 144 93 4060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084045
X-RAY DIFFRACTIONf_angle_d1.5965466
X-RAY DIFFRACTIONf_dihedral_angle_d21.3631520
X-RAY DIFFRACTIONf_chiral_restr0.151596
X-RAY DIFFRACTIONf_plane_restr0.004678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.9220.31021170.26172230X-RAY DIFFRACTION84
2.922-3.14740.35791280.24062455X-RAY DIFFRACTION92
3.1474-3.46390.30041350.21382577X-RAY DIFFRACTION96
3.4639-3.96440.27721340.18062597X-RAY DIFFRACTION98
3.9644-4.99210.19371580.14852639X-RAY DIFFRACTION99
4.9921-33.66150.23591410.17542699X-RAY DIFFRACTION99

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