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- PDB-4xnh: Crystal structure of yeast N-terminal acetyltransferase NatE (IP6... -

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Basic information

Entry
Database: PDB / ID: 4xnh
TitleCrystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a bisubstrate
Components
  • (N-terminal acetyltransferase A complex subunit ...) x 2
  • ACYH8
  • N-terminal acetyltransferase A complex catalytic subunit ARD1
KeywordsTRANSFERASE / N-terminal acetyltransferase / bisubstrate / inositol hexaxisphosphate
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 / N-terminal amino-acid Nalpha-acetyltransferase NatA / Opioid Signalling / 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 / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / 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 / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / Tetratricopeptide repeat / Aminopeptidase / Tetratricopeptide-like helical domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / CARBOXYMETHYL COENZYME *A / INOSITOL HEXAKISPHOSPHATE / 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: 2.1 Å
AuthorsDong, J. / Wang, S. / York, J.D.
CitationJournal: To Be Published
Title: Crystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a bisubstrate
Authors: Dong, J. / Wang, S. / York, J.D.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 2.0Oct 14, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_oper_list.symmetry_operation / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
F: ACYH8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,7927
Polymers147,4974
Non-polymers2,2953
Water12,106672
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-44 kcal/mol
Surface area49500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.475, 114.515, 146.978
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, 2 molecules AC

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


Mass: 99050.133 Da / Num. of mol.: 1
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.: 1
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, 2 molecules BF

#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.: 1
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 ACYH8


Mass: 1058.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01189*PLUS

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Non-polymers , 4 types, 675 molecules

#5: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#6: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#7: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O18P3S
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 14% PEG 400, 0.1 M MES, pH 6.0 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 82940 / % possible obs: 99.7 % / Redundancy: 7.3 % / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.1→40.595 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 3623 5.04 %
Rwork0.1682 --
obs0.1713 71932 85.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→40.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9292 0 138 672 10102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139677
X-RAY DIFFRACTIONf_angle_d1.40813094
X-RAY DIFFRACTIONf_dihedral_angle_d15.043637
X-RAY DIFFRACTIONf_chiral_restr0.0791423
X-RAY DIFFRACTIONf_plane_restr0.0061657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12760.2749530.18211035X-RAY DIFFRACTION34
2.1276-2.15680.2767730.17541228X-RAY DIFFRACTION41
2.1568-2.18760.2394810.17861357X-RAY DIFFRACTION46
2.1876-2.22030.2264680.1741500X-RAY DIFFRACTION49
2.2203-2.25490.2848880.18521596X-RAY DIFFRACTION53
2.2549-2.29190.2519930.18941852X-RAY DIFFRACTION61
2.2919-2.33140.26691120.18762135X-RAY DIFFRACTION71
2.3314-2.37380.27331410.18232537X-RAY DIFFRACTION84
2.3738-2.41950.26351440.19012872X-RAY DIFFRACTION94
2.4195-2.46880.26351460.1762940X-RAY DIFFRACTION98
2.4688-2.52250.22541630.17513015X-RAY DIFFRACTION99
2.5225-2.58120.27411520.17243033X-RAY DIFFRACTION100
2.5812-2.64570.24991700.17313032X-RAY DIFFRACTION100
2.6457-2.71720.26631560.17413047X-RAY DIFFRACTION100
2.7172-2.79720.2371480.18083058X-RAY DIFFRACTION100
2.7972-2.88750.25021740.1833024X-RAY DIFFRACTION100
2.8875-2.99060.24321550.18913065X-RAY DIFFRACTION100
2.9906-3.11030.26111720.19413060X-RAY DIFFRACTION100
3.1103-3.25180.29631420.1843084X-RAY DIFFRACTION100
3.2518-3.42320.23841740.18153034X-RAY DIFFRACTION100
3.4232-3.63750.21821640.16283082X-RAY DIFFRACTION100
3.6375-3.91820.21321830.15073060X-RAY DIFFRACTION100
3.9182-4.31210.19371660.13663106X-RAY DIFFRACTION100
4.3121-4.93510.18541550.12993131X-RAY DIFFRACTION100
4.9351-6.21410.20121710.16643150X-RAY DIFFRACTION100
6.2141-40.60210.18181790.17273276X-RAY DIFFRACTION100

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