[English] 日本語
Yorodumi
- PDB-4q2j: A novel structure-based mechanism for DNA-binding of SATB1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q2j
TitleA novel structure-based mechanism for DNA-binding of SATB1
ComponentsDNA-binding protein SATB1
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


reflex / CD8-positive, alpha-beta T cell differentiation / heterochromatin => GO:0000792 / Apoptotic cleavage of cellular proteins / SUMOylation of chromatin organization proteins / : / CD4-positive, alpha-beta T cell differentiation / activated T cell proliferation / epidermis development / T cell activation ...reflex / CD8-positive, alpha-beta T cell differentiation / heterochromatin => GO:0000792 / Apoptotic cleavage of cellular proteins / SUMOylation of chromatin organization proteins / : / CD4-positive, alpha-beta T cell differentiation / activated T cell proliferation / epidermis development / T cell activation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PML body / nuclear matrix / DNA-binding transcription repressor activity, RNA polymerase II-specific / chromatin organization / nuclear body / chromatin remodeling / DNA-binding transcription factor activity / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
SATB, ubiquitin-like oligomerisation domain / SATB, CULT domain / SATB, CUT1-like DNA-binding domain / SATB, ubiquitin-like oligomerisation domain / SATB, CUTL domain superfamily / SATB, ULD domain superfamily / DNA-binding protein SATB1/SATB2 / Ubiquitin-like oligomerisation domain of SATB / CUT1-like DNA-binding domain of SATB / CUT domain ...SATB, ubiquitin-like oligomerisation domain / SATB, CULT domain / SATB, CUT1-like DNA-binding domain / SATB, ubiquitin-like oligomerisation domain / SATB, CUTL domain superfamily / SATB, ULD domain superfamily / DNA-binding protein SATB1/SATB2 / Ubiquitin-like oligomerisation domain of SATB / CUT1-like DNA-binding domain of SATB / CUT domain / CUT domain / CUT domain profile. / CUT / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-binding protein SATB1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsWang, Z. / Long, J. / Yang, X. / Shen, Y.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Crystal structure of the ubiquitin-like domain-CUT repeat-like tandem of special AT-rich sequence binding protein 1 (SATB1) reveals a coordinating DNA-binding mechanism.
Authors: Wang, Z. / Yang, X. / Guo, S. / Yang, Y. / Su, X.C. / Shen, Y. / Long, J.
History
DepositionApr 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding protein SATB1
B: DNA-binding protein SATB1
C: DNA-binding protein SATB1
D: DNA-binding protein SATB1


Theoretical massNumber of molelcules
Total (without water)80,9334
Polymers80,9334
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-26 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.978, 91.971, 100.239
Angle α, β, γ (deg.)90.00, 128.97, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
DNA-binding protein SATB1 / Special AT-rich sequence-binding protein 1


Mass: 20233.143 Da / Num. of mol.: 4 / Fragment: N-terminal domain, UNP RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Satb1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60611
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% polyethylene glycol 3350, 0.1M sodium malonate pH 7.0, 0.2M glycine, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 25454 / % possible obs: 72.14 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.054 / Rsym value: 0.077 / Net I/σ(I): 16.1
Reflection shellResolution: 2.6→2.69 Å / % possible all: 94.8

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASER2.4phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.603→42.472 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 33.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 1266 4.97 %RANDOM
Rwork0.2278 ---
all0.2299 ---
obs0.2301 19988 90.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.611 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.2191 Å20 Å2-1.7662 Å2
2--35.9066 Å20 Å2
3----18.6875 Å2
Refinement stepCycle: LAST / Resolution: 2.603→42.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4021 0 0 13 4034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094108
X-RAY DIFFRACTIONf_angle_d1.3095581
X-RAY DIFFRACTIONf_dihedral_angle_d19.3581474
X-RAY DIFFRACTIONf_chiral_restr0.085657
X-RAY DIFFRACTIONf_plane_restr0.005702
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6032-2.70750.42151240.3202210072
2.7075-2.83070.40021380.3017237780
2.8307-2.97990.36511190.2778247184
2.9799-3.16650.37071360.2609269591
3.1665-3.41090.2711300.2463283496
3.4109-3.7540.27161480.2328287697
3.754-4.29670.27281420.199290998
4.2967-5.41160.20621710.1988293599
5.4116-42.47780.24671580.2165299199

+
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