[English] 日本語
Yorodumi
- PDB-4hny: Apo N-terminal acetyltransferase complex A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hny
TitleApo N-terminal acetyltransferase complex A
Components
  • N-terminal acetyltransferase A complex catalytic subunit ARD1
  • N-terminal acetyltransferase A complex subunit NAT1
KeywordsTRANSFERASE / TPR/GNAT / N-terminal acetyltransferase
Function / homology
Function and homology information


protein-N-terminal-glutamate acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / NatA complex / protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / acetyltransferase activator activity / ribosome binding / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
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 / Aminopeptidase ...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 / Aminopeptidase / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-terminal acetyltransferase A complex catalytic subunit ARD1 / N-terminal acetyltransferase A complex subunit NAT1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsNeubauer, J.L. / Immormino, R.M. / Dollins, D.E. / Endo-Streeter, S.T. / Pemble IV, C.W. / York, J.D.
CitationJournal: To be Published
Title: The Protein Complex NatA Binds Inositol Hexakisphosphate and Exhibits Conformational Flexibility
Authors: Neubauer, J.L. / Pham, T. / Immormino, R.M. / Dollins, D.E. / Endo-Streeter, S.T. / Li, S. / Pemble IV, C.W. / York, J.D.
History
DepositionOct 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 NAT1
D: N-terminal acetyltransferase A complex catalytic subunit ARD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,36312
Polymers257,9114
Non-polymers1,4528
Water17,763986
1
A: N-terminal acetyltransferase A complex subunit NAT1
B: N-terminal acetyltransferase A complex catalytic subunit ARD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,0198
Polymers128,9562
Non-polymers1,0636
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-31 kcal/mol
Surface area40860 Å2
MethodPISA
2
C: N-terminal acetyltransferase A complex subunit NAT1
D: N-terminal acetyltransferase A complex catalytic subunit ARD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,3444
Polymers128,9562
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-33 kcal/mol
Surface area42560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.416, 129.416, 171.783
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

-
Components

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


Mass: 100134.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: NAT1, AAA1, YDL040C, D2720 / Plasmid: 22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P12945
#2: Protein N-terminal acetyltransferase A complex catalytic subunit ARD1 / NatA complex subunit ARD1 / Arrest-defective protein 1


Mass: 28821.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: ARD1, YHR013C / Plasmid: 30b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P07347, EC: 2.3.1.88
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 986 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5-25% PEG3350, 0.1 M di-ammonium hydrogen phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.249→50 Å / Num. obs: 152807 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.081
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 2.35 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.phaser: 1.7.2_869)model building
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.2_869phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.249→30.158 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 1849 1.27 %
Rwork0.1784 --
obs0.179 145753 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.746 Å2-0 Å2-0 Å2
2--2.746 Å2-0 Å2
3----5.492 Å2
Refinement stepCycle: LAST / Resolution: 2.249→30.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14949 0 81 986 16016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815371
X-RAY DIFFRACTIONf_angle_d0.96420820
X-RAY DIFFRACTIONf_dihedral_angle_d14.2235523
X-RAY DIFFRACTIONf_chiral_restr0.0382320
X-RAY DIFFRACTIONf_plane_restr0.0052683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2493-2.31010.30041310.219610099X-RAY DIFFRACTION86
2.3101-2.3780.25891340.20110346X-RAY DIFFRACTION90
2.378-2.45480.2591230.193810524X-RAY DIFFRACTION91
2.4548-2.54240.24451340.187810750X-RAY DIFFRACTION92
2.5424-2.64420.22931390.181610897X-RAY DIFFRACTION94
2.6442-2.76440.22971450.183610977X-RAY DIFFRACTION95
2.7644-2.91010.23231450.182711192X-RAY DIFFRACTION96
2.9101-3.09220.23591530.185511316X-RAY DIFFRACTION98
3.0922-3.33070.23141540.191211501X-RAY DIFFRACTION99
3.3307-3.66540.22961440.174111540X-RAY DIFFRACTION100
3.6654-4.19460.20331470.158511593X-RAY DIFFRACTION100
4.1946-5.28010.17831440.157711576X-RAY DIFFRACTION100
5.2801-30.16120.19711560.184511593X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.54980.29721.16082.39880.244.80160.40320.5831-0.177-0.772-0.05250.6498-0.1504-0.5447-0.3230.48490.1086-0.19240.46740.04640.598730.8212-54.9653-19.0878
20.76060.02790.28080.77910.11181.12460.0415-0.0435-0.02450.02210.01210.0685-0.0223-0.0254-0.05360.0990.02420.04790.14910.00630.158959.4036-38.222110.4774
31.6839-1.45540.56661.6461-0.32751.1142-0.1772-0.34-0.0360.11990.18390.1385-0.2558-0.5521-0.01280.20220.12620.02330.4296-0.00090.245230.5882-23.69121.56
46.10280.18982.27536.19350.38876.3984-0.23140.68650.3664-0.68850.05070.3163-0.5799-0.01380.13690.23160.00790.00240.19930.03250.20856.7685-38.139-0.2048
53.94110.88013.46423.66012.4824.95580.09450.0524-0.1585-0.2415-0.070.1523-0.1975-0.12420.03420.1722-0.00510.05610.1227-0.00280.190656.8349-46.5415-1.5967
65.37072.22990.24136.2088-1.87835.92790.1662-1.22240.58571.1240.02350.1938-0.7894-0.1504-0.1520.48620.061-0.01620.4114-0.03120.397951.2459-25.81148.1888
70.5776-1.6005-0.31045.25970.06930.9666-0.2628-0.7985-0.40940.70330.3166-0.437-0.0960.083-0.11510.36540.1781-0.070.46760.01140.385240.268-18.70357.3936
83.8181-0.3626-0.56616.72711.06913.5854-0.04540.1612-0.1368-0.5309-0.01930.3596-0.1712-0.110.09220.1111-0.01790.01990.13590.05260.104165.4672-41.7103-1.5904
91.23030.5218-1.27881.3482-1.51624.463-0.0727-0.028-0.1741-0.1211-0.013-0.21450.20140.33830.11340.12810.00570.00340.1325-0.01660.193275.6793-45.9345-5.0311
109.7864.65-6.25616.4551-6.01652.0223-0.3463-0.2371-0.62050.158-0.3668-0.76960.04560.88790.76630.38850.0005-0.04040.46910.03830.279977.3202-50.835720.2418
112.00254.31115.67887.53150.76852.0020.1609-0.6974-0.46080.85870.2427-0.69850.14580.8496-0.31810.47310.172-0.02370.63160.00810.322174.9913-49.481236.0526
120.88370.263-0.07631.858-0.26450.94930.07290.0735-0.04810.0509-0.0102-0.1834-0.02920.0723-0.06280.16280.06560.02040.1922-0.05760.18814.9819-9.724444.5016
133.5249-0.5805-0.3570.35030.00140.38640.04480.1575-0.085-0.0219-0.0592-0.06930.00170.10330.01260.16240.0208-0.01460.16660.01990.187832.5537-22.376946.3615
146.36261.03121.84537.2844-2.12125.20360.0687-0.2705-0.01090.4656-0.2107-0.4446-0.09630.38880.09340.13960.0690.05670.2403-0.00320.20496.2801-4.97547.7528
151.70142.6125-2.22036.4008-5.29818.81210.1033-0.23090.07430.2691-0.244-0.2795-0.16110.51850.13380.13290.0370.00790.1561-0.01970.1842-0.5247-9.349950.8667
167.9375-2.8316-2.75191.00520.97720.95090.86820.9451.5083-0.5161-0.2861-0.3016-0.7454-0.2551-0.550.50240.08770.08560.41750.04450.523922.0824-5.360942.0154
175.2398-2.85790.69281.6251-0.22220.06090.41290.64870.5692-0.0991-0.2944-0.43580.002-0.0053-0.09640.19120.01480.00080.1690.01390.2414.5608-7.935145.3216
181.124-0.36470.21251.41251.07521.6860.3745-0.10140.18960.6422-0.16990.0312-0.6821-0.1977-0.14910.5475-0.00530.06780.17780.02350.2249-7.92035.591454.0874
199.11947.357-9.56689.903-9.74992.00580.03890.87410.7547-0.40910.34290.9172-0.4-1.1727-0.38520.31750.1419-0.0010.39540.04360.3194-16.78783.378340.4397
201.0878-0.1579-0.7750.5631-1.8367.9269-0.1478-0.0928-0.06490.17340.1742-0.0739-0.6573-0.467-0.00590.34140.038-0.01850.35180.01970.2372-13.39665.261418.0226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 54:140 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 141:496 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 497:862 )
4X-RAY DIFFRACTION4(CHAIN B AND RESID 2:29 )
5X-RAY DIFFRACTION5(CHAIN B AND RESID 30:50 )
6X-RAY DIFFRACTION6(CHAIN B AND RESID 51:65 )
7X-RAY DIFFRACTION7(CHAIN B AND RESID 66:89 )
8X-RAY DIFFRACTION8(CHAIN B AND RESID 90:128 )
9X-RAY DIFFRACTION9(CHAIN B AND RESID 129:204 )
10X-RAY DIFFRACTION10(CHAIN B AND RESID 205:223 )
11X-RAY DIFFRACTION11(CHAIN B AND RESID 224:235 )
12X-RAY DIFFRACTION12(CHAIN C AND RESID 25:496 )
13X-RAY DIFFRACTION13(CHAIN C AND RESID 497:862 )
14X-RAY DIFFRACTION14(CHAIN D AND RESID 2:29 )
15X-RAY DIFFRACTION15(CHAIN D AND RESID 30:50 )
16X-RAY DIFFRACTION16(CHAIN D AND RESID 51:70 )
17X-RAY DIFFRACTION17(CHAIN D AND RESID 71:100 )
18X-RAY DIFFRACTION18(CHAIN D AND RESID 101:193 )
19X-RAY DIFFRACTION19(CHAIN D AND RESID 194:204 )
20X-RAY DIFFRACTION20(CHAIN D AND RESID 205:239 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more