[English] 日本語
Yorodumi
- PDB-1sbx: Crystal structure of the Dachshund-homology domain of human SKI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sbx
TitleCrystal structure of the Dachshund-homology domain of human SKI
ComponentsSki oncogene
KeywordsONCOPROTEIN / winged helix / forkhead
Function / homology
Function and homology information


nose morphogenesis / histone deacetylase inhibitor activity / myotube differentiation / lens morphogenesis in camera-type eye / negative regulation of Schwann cell proliferation / camera-type eye morphogenesis / olfactory bulb development / Signaling by BMP / myelination in peripheral nervous system / negative regulation of activin receptor signaling pathway ...nose morphogenesis / histone deacetylase inhibitor activity / myotube differentiation / lens morphogenesis in camera-type eye / negative regulation of Schwann cell proliferation / camera-type eye morphogenesis / olfactory bulb development / Signaling by BMP / myelination in peripheral nervous system / negative regulation of activin receptor signaling pathway / bone morphogenesis / camera-type eye development / embryonic limb morphogenesis / face morphogenesis / anterior/posterior axis specification / cardiac muscle cell proliferation / positive regulation of DNA binding / negative regulation of SMAD protein signal transduction / roof of mouth development / SMAD binding / somatic stem cell population maintenance / positive regulation of Wnt signaling pathway / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / skeletal muscle fiber development / negative regulation of fibroblast proliferation / transcription repressor complex / transforming growth factor beta receptor signaling pathway / neural tube closure / cell motility / Downregulation of SMAD2/3:SMAD4 transcriptional activity / negative regulation of transforming growth factor beta receptor signaling pathway / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / retina development in camera-type eye / DNA-binding transcription factor binding / transcription regulator complex / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ski / : / c-SKI SMAD4-binding domain / Transcription regulator SKI/SnoN / c-SKI Smad4 binding domain / c-SKI Smad4 binding domain / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC family / Mlu1-box Binding Protein; DNA-binding Domain ...Ski / : / c-SKI SMAD4-binding domain / Transcription regulator SKI/SnoN / c-SKI Smad4 binding domain / c-SKI Smad4 binding domain / SKI/SNO/DAC domain / Ski-like, DNA-binding domain superfamily / SKI/SNO/DAC family / Mlu1-box Binding Protein; DNA-binding Domain / SAND-like domain superfamily / Putative DNA-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsWilson, J.J. / Malakhova, M. / Zhang, R. / Joachimiak, A. / Hegde, R.S.
CitationJournal: Structure / Year: 2004
Title: Crystal Structure of the Dachshund Homology Domain of human SKI
Authors: Wilson, J.J. / Malakhova, M. / Zhang, R. / Joachimiak, A. / Hegde, R.S.
History
DepositionFeb 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ski oncogene


Theoretical massNumber of molelcules
Total (without water)11,8671
Polymers11,8671
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.927, 46.633, 35.729
Angle α, β, γ (deg.)90.00, 93.97, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ski oncogene / C-ski


Mass: 11867.272 Da / Num. of mol.: 1 / Fragment: Dachshund-homology domain of human SKI
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKI / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P12755
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.82 Å3/Da / Density % sol: 32.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5
Details: PEG 3350, pH 5.5, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97834, 0.97852, 0.95372
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 3, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978341
20.978521
30.953721
ReflectionResolution: 1.5→50 Å / Num. all: 20103 / Num. obs: 19541 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 9.8 Å2 / Rsym value: 0.107
Reflection shellResolution: 1.5→1.55 Å / % possible all: 67.6

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→22.62 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 547143.35 / Data cutoff high rms absF: 547143.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1817 9.3 %RANDOM
Rwork0.17 ---
all0.184 20103 --
obs0.184 19541 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9922 Å2 / ksol: 0.387636 e/Å3
Displacement parametersBiso mean: 9 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0.23 Å2
2--0.58 Å20 Å2
3----1.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.65→22.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms865 0 0 79 944
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.572
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.214 281 8.9 %
Rwork0.202 2873 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

+
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