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- PDB-6wf3: Crystal structure of human Naa50 in complex with a cofactor deriv... -

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Basic information

Entry
Database: PDB / ID: 6wf3
TitleCrystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1)
Components
  • ACE-MET-LEU-GLY-PRO-NH2
  • N-alpha-acetyltransferase 50
KeywordsTRANSFERASE/INHIBITOR / N-alpha-acetyltransferase 50 / Inhibitor complex / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / protein-lysine-acetyltransferase activity / mitotic sister chromatid cohesion ...mitotic sister chromatid cohesion, centromeric / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal protein amino acid acetylation / NatA complex / protein N-terminal-methionine acetyltransferase activity / protein-N-terminal amino-acid acetyltransferase activity / histone H4 acetyltransferase activity / establishment of mitotic sister chromatid cohesion / protein-lysine-acetyltransferase activity / mitotic sister chromatid cohesion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleolus / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 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 50
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.291 Å
AuthorsGreasley, S.E. / Feng, J. / Deng, Y.-L. / Stewart, A.E.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Characterization of SpecificN-alpha-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library.
Authors: Kung, P.P. / Bingham, P. / Burke, B.J. / Chen, Q. / Cheng, X. / Deng, Y.L. / Dou, D. / Feng, J. / Gallego, G.M. / Gehring, M.R. / Grant, S.K. / Greasley, S. / Harris, A.R. / Maegley, K.A. / ...Authors: Kung, P.P. / Bingham, P. / Burke, B.J. / Chen, Q. / Cheng, X. / Deng, Y.L. / Dou, D. / Feng, J. / Gallego, G.M. / Gehring, M.R. / Grant, S.K. / Greasley, S. / Harris, A.R. / Maegley, K.A. / Meier, J. / Meng, X. / Montano, J.L. / Morgan, B.A. / Naughton, B.S. / Palde, P.B. / Paul, T.A. / Richardson, P. / Sakata, S. / Shaginian, A. / Sonnenburg, W.K. / Subramanyam, C. / Timofeevski, S. / Wan, J. / Yan, W. / Stewart, A.E.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-alpha-acetyltransferase 50
B: N-alpha-acetyltransferase 50
C: N-alpha-acetyltransferase 50
D: N-alpha-acetyltransferase 50
E: N-alpha-acetyltransferase 50
F: N-alpha-acetyltransferase 50
G: ACE-MET-LEU-GLY-PRO-NH2
H: ACE-MET-LEU-GLY-PRO-NH2
I: ACE-MET-LEU-GLY-PRO-NH2
J: ACE-MET-LEU-GLY-PRO-NH2
K: ACE-MET-LEU-GLY-PRO-NH2
L: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,67818
Polymers120,07212
Non-polymers4,6056
Water6,377354
1
A: N-alpha-acetyltransferase 50
G: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7803
Polymers20,0122
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-7 kcal/mol
Surface area8080 Å2
MethodPISA
2
B: N-alpha-acetyltransferase 50
H: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7803
Polymers20,0122
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-7 kcal/mol
Surface area8160 Å2
MethodPISA
3
C: N-alpha-acetyltransferase 50
I: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7803
Polymers20,0122
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-7 kcal/mol
Surface area8060 Å2
MethodPISA
4
D: N-alpha-acetyltransferase 50
J: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7803
Polymers20,0122
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-7 kcal/mol
Surface area8150 Å2
MethodPISA
5
E: N-alpha-acetyltransferase 50
K: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7803
Polymers20,0122
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-7 kcal/mol
Surface area8080 Å2
MethodPISA
6
F: N-alpha-acetyltransferase 50
L: ACE-MET-LEU-GLY-PRO-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7803
Polymers20,0122
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-7 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.547, 124.17, 109.085
Angle α, β, γ (deg.)90, 100.92, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-alpha-acetyltransferase 50 / hNaa50p / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog ...hNaa50p / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog / hSAN / N-epsilon-acetyltransferase 50 / NatE catalytic subunit / Naa50


Mass: 19571.502 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAA50, MAK3, NAT13, NAT5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZZ1, N-terminal methionine Nalpha-acetyltransferase NatE, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide
ACE-MET-LEU-GLY-PRO-NH2


Mass: 440.581 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 286.15 K / Method: vapor diffusion, sitting drop
Details: Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1: ...Details: Naa50 apo protein (14.3 mg/ml) was incubated with compound 1 in a 1:3 molar ratio on ice for 60 min. Reservoir solution containing 0.2 M ammonium sulfate and 30% (w/v) PEG 3K/4K was mixed 1:1 with protein/ligand complex

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→53.71 Å / Num. obs: 56682 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13
Reflection shellResolution: 2.29→2.41 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.52 / Num. unique obs: 8301 / CC1/2: 0.785 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Ob0

2ob0


Resolution: 2.291→53.71 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.882 / SU R Cruickshank DPI: 0.286 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.273 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.211
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 2880 -RANDOM
Rwork0.208 ---
obs0.2097 56653 99.4 %-
Displacement parametersBiso mean: 56.03 Å2
Baniso -1Baniso -2Baniso -3
1--22.8502 Å20 Å25.8757 Å2
2--16.4096 Å20 Å2
3---6.4406 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.291→53.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 474 354 8148
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088334HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0111652HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2928SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1356HARMONIC5
X-RAY DIFFRACTIONt_it7956HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1008SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5722SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion17.98
LS refinement shellResolution: 2.291→2.31 Å
RfactorNum. reflection% reflection
Rfree0.3114 59 -
Rwork0.263 --
obs--99.82 %

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