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- PDB-5icv: Crystal structure of human NatF (hNaa60) bound to a bisubstrate a... -

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Basic information

Entry
Database: PDB / ID: 5icv
TitleCrystal structure of human NatF (hNaa60) bound to a bisubstrate analogue
Components
  • MET-LYS-ALA-VAL-LIG
  • N-alpha-acetyltransferase 60
KeywordsTRANSFERASE / Acetylation / GNAT / NAT
Function / homology
Function and homology information


N-terminal peptidyl-methionine acetylation / N-terminal methionine Nalpha-acetyltransferase NatF / N-terminal protein amino acid acetylation / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / histone H4 acetyltransferase activity / histone acetyltransferase activity / histone acetyltransferase / chromosome segregation / nucleosome assembly ...N-terminal peptidyl-methionine acetylation / N-terminal methionine Nalpha-acetyltransferase NatF / N-terminal protein amino acid acetylation / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / histone H4 acetyltransferase activity / histone acetyltransferase activity / histone acetyltransferase / chromosome segregation / nucleosome assembly / cell population proliferation / Golgi membrane / protein homodimerization activity
Similarity search - Function
N-alpha-acetyltransferase 60-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1XE / N-alpha-acetyltransferase 60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsStove, S.I. / Magin, R.S. / Marmorstein, R. / Arnesen, T.
Funding support Norway, United States, 5items
OrganizationGrant numberCountry
Norwegian Cancer Society Norway
The Bergen Research Foundation BFS Norway
Research Council of Norway Norway
National Institutes of HealthGM060293 United States
National Institutes of HealthGM071339 United States
CitationJournal: Structure / Year: 2016
Title: Crystal Structure of the Golgi-Associated Human N alpha-Acetyltransferase 60 Reveals the Molecular Determinants for Substrate-Specific Acetylation.
Authors: Stve, S.I. / Magin, R.S. / Foyn, H. / Haug, B.E. / Marmorstein, R. / Arnesen, T.
History
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Jan 10, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-alpha-acetyltransferase 60
B: N-alpha-acetyltransferase 60
C: MET-LYS-ALA-VAL-LIG
D: MET-LYS-ALA-VAL-LIG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6196
Polymers41,9764
Non-polymers1,6432
Water6,936385
1
A: N-alpha-acetyltransferase 60
C: MET-LYS-ALA-VAL-LIG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8093
Polymers20,9882
Non-polymers8221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-9 kcal/mol
Surface area9340 Å2
MethodPISA
2
B: N-alpha-acetyltransferase 60
D: MET-LYS-ALA-VAL-LIG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8093
Polymers20,9882
Non-polymers8221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-9 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.448, 48.448, 148.368
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein N-alpha-acetyltransferase 60 / Histone acetyltransferase type B protein 4 / HAT4 / N-acetyltransferase 15 / NatF catalytic subunit


Mass: 20539.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA60, HAT4, NAT15, UNQ2771/PRO7155 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H7X0, histone acetyltransferase, EC: 2.3.1.88
#2: Protein/peptide MET-LYS-ALA-VAL-LIG


Mass: 448.599 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-1XE / [5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)furan-2-yl]methyl (3R)-4-{[3-({(E)-2-[(2,2-dihydroxyethyl)sulfanyl]ethenyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate


Mass: 821.538 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H34N7O18P3S / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 4% Tascimate pH 4.0 and 12% PEG 3500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→40.564 Å / Num. obs: 51410 / % possible obs: 99.8 % / Redundancy: 13 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 18.62
Reflection shellResolution: 1.53→1.568 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.635 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LX9

4lx9


Resolution: 1.53→40.564 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7
RfactorNum. reflection% reflection
Rfree0.2084 2009 3.93 %
Rwork0.1905 --
obs0.1912 51149 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→40.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 0 385 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073113
X-RAY DIFFRACTIONf_angle_d1.2844244
X-RAY DIFFRACTIONf_dihedral_angle_d16.9291136
X-RAY DIFFRACTIONf_chiral_restr0.044468
X-RAY DIFFRACTIONf_plane_restr0.004521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5298-1.5680.30821420.26363506X-RAY DIFFRACTION99
1.568-1.61040.34521450.24813471X-RAY DIFFRACTION100
1.6104-1.65780.29531420.24583504X-RAY DIFFRACTION100
1.6578-1.71130.29971410.243514X-RAY DIFFRACTION100
1.7113-1.77250.23551440.23443492X-RAY DIFFRACTION99
1.7725-1.84340.30171480.22663491X-RAY DIFFRACTION100
1.8434-1.92730.25641390.21523516X-RAY DIFFRACTION100
1.9273-2.02890.22881450.20533548X-RAY DIFFRACTION100
2.0289-2.15610.23271430.19273498X-RAY DIFFRACTION100
2.1561-2.32250.24181460.19163543X-RAY DIFFRACTION100
2.3225-2.55620.2131370.19643530X-RAY DIFFRACTION100
2.5562-2.9260.22141470.19223498X-RAY DIFFRACTION100
2.926-3.68610.1731420.16743531X-RAY DIFFRACTION100
3.6861-40.5780.16011480.16673498X-RAY DIFFRACTION98

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