[English] 日本語
Yorodumi
- PDB-1qsn: CRYSTAL STRUCTURE OF TETRAHYMENA GCN5 WITH BOUND COENZYME A AND H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qsn
TitleCRYSTAL STRUCTURE OF TETRAHYMENA GCN5 WITH BOUND COENZYME A AND HISTONE H3 PEPTIDE
Components
  • HISTONE H3
  • TGCN5 HISTONE ACETYL TRANSFERASE
KeywordsTRANSFERASE / HISTONE ACETYLTRANSFERASE / GCN5-RELATED N-ACETYLTRANSFERASE / COA-BINDING PROTEIN / TERNARY COMPLEX
Function / homology
Function and homology information


sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / : / : / Assembly of the ORC complex at the origin of replication / histone H3 acetyltransferase activity / Oxidative Stress Induced Senescence ...sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / : / : / Assembly of the ORC complex at the origin of replication / histone H3 acetyltransferase activity / Oxidative Stress Induced Senescence / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / histone acetyltransferase complex / intracellular copper ion homeostasis / histone acetyltransferase / CENP-A containing nucleosome / aerobic respiration / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Bromodomain, conserved site / Bromodomain signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Histone-fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Histone H3 / histone acetyltransferase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsRojas, J.R. / Trievel, R.C. / Zhou, J. / Mo, Y. / Li, X. / Berger, S.L. / David Allis, C. / Marmorstein, R.
CitationJournal: Nature / Year: 1999
Title: Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide.
Authors: Rojas, J.R. / Trievel, R.C. / Zhou, J. / Mo, Y. / Li, X. / Berger, S.L. / Allis, C.D. / Marmorstein, R.
History
DepositionJun 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: TGCN5 HISTONE ACETYL TRANSFERASE
B: HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2733
Polymers20,5062
Non-polymers7681
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-5 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.090, 65.090, 96.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein TGCN5 HISTONE ACETYL TRANSFERASE


Mass: 19344.500 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Plasmid: PRSET A / Production host: Escherichia coli (E. coli)
References: UniProt: Q27198, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide HISTONE H3


Mass: 1161.355 Da / Num. of mol.: 1 / Fragment: 11 MER PEPTIDE (RESIDUES 9 - 19) / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61830
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: TRIS, AMMONIUM SULFATE, MANGANESE CHLORIDE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mlprotein1drop
21 mMCoA1drop
31.5 mMpeptide1drop
41.6 Mammonium sulfate1reservoir
550 mMTris1reservoir
610 mM1reservoirMnCl2

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.917
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 13391 / Num. obs: 12960 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 33.3
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.066 / % possible all: 77.9
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Num. measured all: 201683
Reflection shell
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 2.21 Å / Redundancy: 5.7 %

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→30 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: USED MAXIMUM LIKELIHOOD ALGORITHM
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1300 -RANDOM
Rwork0.239 ---
obs0.239 12960 96.4 %-
all-13064 --
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 48 122 1602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

+
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