[English] 日本語
Yorodumi
- PDB-3tfy: Naa50p amino-terminal acetyltransferase bound to substrate peptid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tfy
TitleNaa50p amino-terminal acetyltransferase bound to substrate peptide fragment and CoA
Components
  • N-alpha-acetyltransferase 50, NatE catalytic subunit
  • hnRNP F
KeywordsTRANSFERASE / GNAT Family / N(alpha)-acetyltransferase
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 / FGFR2 alternative splicing / 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 / FGFR2 alternative splicing / mitotic sister chromatid cohesion / protein-lysine-acetyltransferase activity / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / catalytic step 2 spliceosome / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mRNA Splicing - Major Pathway / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / post-translational protein modification / mRNA splicing, via spliceosome / single-stranded RNA binding / ribonucleoprotein complex / synapse / nucleolus / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Zinc finger, CHHC-type / RNPHF zinc finger / : / : / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase ...Zinc finger, CHHC-type / RNPHF zinc finger / : / : / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Heterogeneous nuclear ribonucleoprotein F / N-alpha-acetyltransferase 50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLiszczak, G.P. / Marmorstein, R.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of a Ternary Naa50p (NAT5/SAN) N-terminal Acetyltransferase Complex Reveals the Molecular Basis for Substrate-specific Acetylation.
Authors: Liszczak, G. / Arnesen, T. / Marmorstein, R.
History
DepositionAug 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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-alpha-acetyltransferase 50, NatE catalytic subunit
D: hnRNP F
B: N-alpha-acetyltransferase 50, NatE catalytic subunit
E: hnRNP F
C: N-alpha-acetyltransferase 50, NatE catalytic subunit
F: hnRNP F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7659
Polymers61,4636
Non-polymers2,3033
Water1,67593
1
A: N-alpha-acetyltransferase 50, NatE catalytic subunit
D: hnRNP F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2553
Polymers20,4882
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-6 kcal/mol
Surface area8780 Å2
MethodPISA
2
B: N-alpha-acetyltransferase 50, NatE catalytic subunit
E: hnRNP F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2553
Polymers20,4882
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-6 kcal/mol
Surface area8470 Å2
MethodPISA
3
C: N-alpha-acetyltransferase 50, NatE catalytic subunit
F: hnRNP F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2553
Polymers20,4882
Non-polymers7681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-7 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.299, 104.103, 68.247
Angle α, β, γ (deg.)90.00, 106.29, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein N-alpha-acetyltransferase 50, NatE catalytic subunit / N-acetyltransferase 13 / N-acetyltransferase 5 / hNAT5 / N-acetyltransferase san homolog / hSAN


Mass: 19427.373 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAK3, NAA50, NAT13, NAT5 / Plasmid: pETM-GST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q9GZZ1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide hnRNP F


Mass: 1060.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / References: UniProt: P52597*PLUS
#3: Chemical ChemComp-COA / COENZYME A


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


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5
Details: well solution: 16% PEG 8000, 20% glycerol, 40mM potassium phosphate (monobasic), pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2010 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 17043 / Num. obs: 16856 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 12.9 / Net I/σ(I): 10.2
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 682 / Rsym value: 40.9 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PSW (cofactor and solvent removed)

2psw


Resolution: 2.75→33.659 Å / SU ML: 0.39 / σ(F): 0.19 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 813 5.08 %
Rwork0.1903 --
obs0.1935 16010 94.69 %
all-17043 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.837 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.8989 Å2-0 Å2-9.188 Å2
2---22.5298 Å20 Å2
3---0.6309 Å2
Refinement stepCycle: LAST / Resolution: 2.75→33.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3823 0 144 93 4060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084045
X-RAY DIFFRACTIONf_angle_d1.5965466
X-RAY DIFFRACTIONf_dihedral_angle_d21.3631520
X-RAY DIFFRACTIONf_chiral_restr0.151596
X-RAY DIFFRACTIONf_plane_restr0.004678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.9220.31021170.26172230X-RAY DIFFRACTION84
2.922-3.14740.35791280.24062455X-RAY DIFFRACTION92
3.1474-3.46390.30041350.21382577X-RAY DIFFRACTION96
3.4639-3.96440.27721340.18062597X-RAY DIFFRACTION98
3.9644-4.99210.19371580.14852639X-RAY DIFFRACTION99
4.9921-33.66150.23591410.17542699X-RAY DIFFRACTION99

+
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