[English] 日本語
Yorodumi
- PDB-4a6q: Crystal structure of mouse SAP18 residues 6-143 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a6q
TitleCrystal structure of mouse SAP18 residues 6-143
ComponentsHISTONE DEACETYLASE COMPLEX SUBUNIT SAP18
KeywordsTRANSCRIPTION / SPLICING / RNA METABOLISM / UBIQUITIN-LIKE
Function / homology
Function and homology information


ASAP complex / HDACs deacetylate histones / mRNA Splicing - Major Pathway / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / histone deacetylase complex / RNA splicing / mRNA processing / transcription corepressor activity / transcription regulator complex ...ASAP complex / HDACs deacetylate histones / mRNA Splicing - Major Pathway / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / histone deacetylase complex / RNA splicing / mRNA processing / transcription corepressor activity / transcription regulator complex / nuclear body / nuclear speck / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol
Similarity search - Function
ASAP complex, SAP18 subunit / Sin3 associated polypeptide p18 / Histone deacetylase complex subunit SAP18 / Sin3 associated polypeptide p18 superfamily / Sin3 associated polypeptide p18 (SAP18) / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Histone deacetylase complex subunit SAP18
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsMurachelli, A.G. / Ebert, J. / Basquin, C. / Le Hir, H. / Conti, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The Structure of the Asap Core Complex Reveals the Existence of a Pinin-Containing Psap Complex
Authors: Murachelli, A.G. / Ebert, J. / Basquin, C. / Le Hir, H. / Conti, E.
History
DepositionNov 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Other
Revision 1.2Mar 18, 2015Group: Data collection / Other / Source and taxonomy

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9213
Polymers16,7431
Non-polymers1782
Water3,279182
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.368, 73.631, 86.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2027-

HOH

-
Components

#1: Protein HISTONE DEACETYLASE COMPLEX SUBUNIT SAP18 / / 18 KDA SIN3-ASSOCIATED POLYPEPTIDE / SIN3-ASSOCIATED POLYPEPTIDE P18


Mass: 16743.186 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: O55128
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGPDSM ARE RESIDUALS FROM CLEAVAGE AND CLONING.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 8 / Details: 25% ISOPROPANOL, 0.1 M BICINE PH 8.0.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9732
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 1.5→56.12 Å / Num. obs: 25887 / % possible obs: 98.9 % / Observed criterion σ(I): 3.7 / Redundancy: 6.6 % / Biso Wilson estimate: 17.19 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.7 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.2_869)refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→56.124 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 18.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 1329 5.14 %
Rwork0.1862 --
obs0.1874 25881 98.71 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.517 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1547 Å20 Å20 Å2
2--2.928 Å20 Å2
3---1.2267 Å2
Refinement stepCycle: LAST / Resolution: 1.5→56.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 12 182 1311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121233
X-RAY DIFFRACTIONf_angle_d1.3561683
X-RAY DIFFRACTIONf_dihedral_angle_d12.598493
X-RAY DIFFRACTIONf_chiral_restr0.097186
X-RAY DIFFRACTIONf_plane_restr0.007218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.56010.3261570.30962617X-RAY DIFFRACTION97
1.5601-1.63110.29621340.24762693X-RAY DIFFRACTION98
1.6311-1.71710.27621430.21892672X-RAY DIFFRACTION99
1.7171-1.82470.22841450.18752695X-RAY DIFFRACTION98
1.8247-1.96550.20331580.17142691X-RAY DIFFRACTION99
1.9655-2.16340.19091680.16912713X-RAY DIFFRACTION99
2.1634-2.47640.18771460.17052761X-RAY DIFFRACTION99
2.4764-3.120.22121490.17492777X-RAY DIFFRACTION100
3.12-56.16320.19041290.18552933X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 21.6734 Å / Origin y: 93.9418 Å / Origin z: 19.1586 Å
111213212223313233
T0.0514 Å2-0.0071 Å20.02 Å2-0.0451 Å2-0.0063 Å2--0.038 Å2
L0.5736 °2-0.1344 °20.1545 °2-0.389 °20.0886 °2--0.4416 °2
S-0.0172 Å °-0.046 Å °-0.002 Å °0.0339 Å °0.012 Å °-0.0469 Å °0.0417 Å °-0.016 Å °0.0039 Å °
Refinement TLS groupSelection details: CHAIN A AND RESID 1:143

+
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