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- PDB-5hh1: Crystal structure of human Naa60 mutant - F34A in complex with CoA -

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Basic information

Entry
Database: PDB / ID: 5hh1
TitleCrystal structure of human Naa60 mutant - F34A in complex with CoA
ComponentsN-alpha-acetyltransferase 60
KeywordsTRANSFERASE / N-terminal acetylation / NATs / Protein modification
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 H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity ...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 H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 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
COENZYME A / N-alpha-acetyltransferase 60
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsChen, J.Y. / Liu, L. / Yun, C.H.
Funding support China, 3items
OrganizationGrant numberCountry
National Basic Research Program of China2012CB917202 China
National Science Foundation of China31270769 China
Ministry of Science and Technology of ChinaNCET-12-0013 China
CitationJournal: Sci Rep / Year: 2016
Title: Structure and function of human Naa60 (NatF), a Golgi-localized bi-functional acetyltransferase
Authors: Chen, J.Y. / Liu, L. / Cao, C.L. / Li, M.J. / Tan, K. / Yang, X. / Yun, C.H.
History
DepositionJan 9, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: 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

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Assembly

Deposited unit
A: N-alpha-acetyltransferase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6592
Polymers22,8921
Non-polymers7681
Water3,027168
1
A: N-alpha-acetyltransferase 60
hetero molecules

A: N-alpha-acetyltransferase 60
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3194
Polymers45,7842
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5030 Å2
ΔGint-14 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.685, 74.031, 43.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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: 22891.914 Da / Num. of mol.: 1 / Fragment: UNP residues 1-199 / Mutation: V4E, V5E, P6R, F34A
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: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293.15 K / Method: liquid diffusion / pH: 8.5
Details: 0.2M Lithium Sulfate monohydrate, 0.1M Tris pH 8.5, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 20501 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 27.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HGZ

5hgz


Resolution: 1.803→43.521 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2093 1054 5.14 %
Rwork0.1888 --
obs0.1898 20490 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.803→43.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 48 168 1782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151707
X-RAY DIFFRACTIONf_angle_d1.5812333
X-RAY DIFFRACTIONf_dihedral_angle_d21.506696
X-RAY DIFFRACTIONf_chiral_restr0.214261
X-RAY DIFFRACTIONf_plane_restr0.006279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8027-1.88480.30781400.29342354X-RAY DIFFRACTION99
1.8848-1.98410.23671380.24712380X-RAY DIFFRACTION100
1.9841-2.10840.23541090.22952409X-RAY DIFFRACTION100
2.1084-2.27120.21191590.2142382X-RAY DIFFRACTION100
2.2712-2.49980.22921210.20912422X-RAY DIFFRACTION100
2.4998-2.86140.23411530.21382416X-RAY DIFFRACTION100
2.8614-3.60480.21931100.18032473X-RAY DIFFRACTION100
3.6048-43.53370.17531240.16142600X-RAY DIFFRACTION100

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