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- PDB-4y49: Crystal structure of yeast N-terminal acetyltransferase (ppGpp) N... -

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Basic information

Entry
Database: PDB / ID: 4y49
TitleCrystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate
Components
  • (N-terminal acetyltransferase A complex subunit ...) x 2
  • ALA-ALA-ALA-ALA-ALA-ALA
  • N-terminal acetyltransferase A complex catalytic subunit ARD1
KeywordsTRANSFERASE / N-terminal acetyltransferase / NatE / ppGpp / bisubstrate
Function / homology
Function and homology information


cellular pigmentation / positive regulation of oxytocin production / Peptide hormone biosynthesis / Defective ACTH causes obesity and POMCD / type 1 melanocortin receptor binding / N-terminal protein amino acid propionylation / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / regulation of corticosterone secretion / peptide-glutamate-alpha-N-acetyltransferase activity ...cellular pigmentation / positive regulation of oxytocin production / Peptide hormone biosynthesis / Defective ACTH causes obesity and POMCD / type 1 melanocortin receptor binding / N-terminal protein amino acid propionylation / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / regulation of corticosterone secretion / peptide-glutamate-alpha-N-acetyltransferase activity / response to melanocyte-stimulating hormone / Opioid Signalling / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal methionine Nalpha-acetyltransferase NatE / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / Androgen biosynthesis / regulation of appetite / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / regulation of glycogen metabolic process / Glucocorticoid biosynthesis / mitotic sister chromatid cohesion / negative regulation of tumor necrosis factor production / neuropeptide signaling pathway / Endogenous sterols / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of cAMP-mediated signaling / Peptide ligand-binding receptors / secretory granule / generation of precursor metabolites and energy / G protein-coupled receptor binding / calcium-mediated signaling / G-protein activation / hormone activity / regulation of blood pressure / ribosome binding / glucose homeostasis / cell-cell signaling / G alpha (i) signalling events / G alpha (s) signalling events / Interleukin-4 and Interleukin-13 signaling / secretory granule lumen / signaling receptor binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Opiodes neuropeptide / Pro-opiomelanocortin N-terminal / Opioids neuropeptide / Pro-opiomelanocortin, N-terminal region / Pro-opiomelanocortin, N-terminal region / Opioids neuropeptide / Pro-opiomelanocortin / Pro-opiomelanocortin/corticotropin, ACTH, central region / Corticotropin ACTH domain / Corticotropin ACTH domain ...Opiodes neuropeptide / Pro-opiomelanocortin N-terminal / Opioids neuropeptide / Pro-opiomelanocortin, N-terminal region / Pro-opiomelanocortin, N-terminal region / Opioids neuropeptide / Pro-opiomelanocortin / Pro-opiomelanocortin/corticotropin, ACTH, central region / Corticotropin ACTH domain / Corticotropin ACTH domain / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Tetratricopeptide repeats / Acyl-CoA N-acyltransferase / Tetratricopeptide repeat / Aminopeptidase / Tetratricopeptide-like helical domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / CARBOXYMETHYL COENZYME *A / GUANOSINE-5',3'-TETRAPHOSPHATE / Pro-opiomelanocortin / N-terminal acetyltransferase A complex catalytic subunit ARD1 / N-terminal acetyltransferase A complex subunit NAT1 / N-alpha-acetyltransferase NAT5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.95 Å
AuthorsDong, J. / Wang, S. / York, J.D.
CitationJournal: To Be Published
Title: Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a bisubstrate
Authors: Dong, J. / Wang, S. / York, J.D.
History
DepositionFeb 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-terminal acetyltransferase A complex subunit NAT1
B: N-terminal acetyltransferase A complex catalytic subunit ARD1
C: N-terminal acetyltransferase A complex subunit NAT5
E: ALA-ALA-ALA-ALA-ALA-ALA
G: N-terminal acetyltransferase A complex subunit NAT1
H: N-terminal acetyltransferase A complex catalytic subunit ARD1
I: N-terminal acetyltransferase A complex subunit NAT5
K: ALA-ALA-ALA-ALA-ALA-ALA
M: N-terminal acetyltransferase A complex subunit NAT1
N: N-terminal acetyltransferase A complex catalytic subunit ARD1
O: N-terminal acetyltransferase A complex subunit NAT5
Q: ALA-ALA-ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,30921
Polymers442,59412
Non-polymers6,7159
Water0
1
A: N-terminal acetyltransferase A complex subunit NAT1
B: N-terminal acetyltransferase A complex catalytic subunit ARD1
C: N-terminal acetyltransferase A complex subunit NAT5
E: ALA-ALA-ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7707
Polymers147,5314
Non-polymers2,2383
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: N-terminal acetyltransferase A complex subunit NAT1
H: N-terminal acetyltransferase A complex catalytic subunit ARD1
I: N-terminal acetyltransferase A complex subunit NAT5
K: ALA-ALA-ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7707
Polymers147,5314
Non-polymers2,2383
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: N-terminal acetyltransferase A complex subunit NAT1
N: N-terminal acetyltransferase A complex catalytic subunit ARD1
O: N-terminal acetyltransferase A complex subunit NAT5
Q: ALA-ALA-ALA-ALA-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7707
Polymers147,5314
Non-polymers2,2383
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.723, 146.486, 254.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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N-terminal acetyltransferase A complex subunit ... , 2 types, 6 molecules AGMCIO

#1: Protein N-terminal acetyltransferase A complex subunit NAT1 / NatA complex subunit NAT1 / Amino-terminal / alpha-amino / acetyltransferase 1


Mass: 99084.195 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P12945
#3: Protein N-terminal acetyltransferase A complex subunit NAT5 / NatA complex subunit NAT5


Mass: 19753.727 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
References: UniProt: Q08689, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Protein / Protein/peptide , 2 types, 6 molecules BHNEKQ

#2: Protein N-terminal acetyltransferase A complex catalytic subunit ARD1 / NatA complex subunit ARD1 / Arrest-defective protein 1


Mass: 27635.168 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P07347, EC: 2.3.1.88
#4: Protein/peptide ALA-ALA-ALA-ALA-ALA-ALA


Mass: 1058.169 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01189*PLUS

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Non-polymers , 3 types, 9 molecules

#5: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp / Guanosine pentaphosphate


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#6: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O18P3S
#7: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H38N7O17P3S

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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: 47.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 17% Jeffamine ED-2001 pH 7.0, 0.1 M imidazole, pH 6.2
PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.95→49.63 Å / Num. obs: 36307 / % possible obs: 97 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.6
Reflection shellResolution: 3.95→4.09 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 4.5 / % possible all: 83.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.95→49.63 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.839 / SU B: 222.871 / SU ML: 1.31 / Cross valid method: THROUGHOUT / ESU R Free: 1.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.42087 1799 5 %RANDOM
Rwork0.35478 ---
obs0.35796 34284 96.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.988 Å2
Baniso -1Baniso -2Baniso -3
1--26.71 Å20 Å20 Å2
2--0.3 Å20 Å2
3---26.41 Å2
Refinement stepCycle: LAST / Resolution: 3.95→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19706 0 414 0 20120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01920248
X-RAY DIFFRACTIONr_bond_other_d0.010.0219063
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.89327866
X-RAY DIFFRACTIONr_angle_other_deg1.249342580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.57953233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.60922.754472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.791151293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.171542
X-RAY DIFFRACTIONr_chiral_restr0.0870.23333
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0225800
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024735
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it00.213077
X-RAY DIFFRACTIONr_mcbond_other00.213075
X-RAY DIFFRACTIONr_mcangle_it00.316254
X-RAY DIFFRACTIONr_mcangle_other00.316255
X-RAY DIFFRACTIONr_scbond_it00.27171
X-RAY DIFFRACTIONr_scbond_other00.27170
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other00.311612
X-RAY DIFFRACTIONr_long_range_B_refined01.70723335
X-RAY DIFFRACTIONr_long_range_B_other01.70723336
X-RAY DIFFRACTIONr_rigid_bond_restr0.012339311
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded0539033
LS refinement shellResolution: 3.949→4.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.577 103 -
Rwork0.401 1941 -
obs--74.9 %
Refinement TLS params.Method: refined / Origin x: 18.4612 Å / Origin y: 43.9326 Å / Origin z: 544.642 Å
111213212223313233
T2.0912 Å20.017 Å20.0177 Å2-0.9986 Å20.0026 Å2--0.0022 Å2
L0.0272 °20.0678 °20.0296 °2-0.177 °20.0628 °2--0.0504 °2
S-0.0055 Å °0.0019 Å °-0.0039 Å °-0.0144 Å °0.0068 Å °-0.0099 Å °-0.0105 Å °0.0018 Å °-0.0013 Å °

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