[English] 日本語
Yorodumi
- PDB-6ht5: Oct4/Sox2:UTF1 structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ht5
TitleOct4/Sox2:UTF1 structure
Components
  • DNA (5'-D(*TP*TP*CP*AP*CP*TP*AP*GP*CP*AP*TP*AP*AP*CP*AP*AP*TP*GP*AP*GP*G)-3')
  • DNA (5'-D(P*CP*CP*TP*CP*AP*TP*TP*GP*TP*TP*AP*TP*GP*CP*TP*AP*GP*TP*GP*AP*AP*G)-3')
  • POU domain, class 5, transcription factor 1
  • Transcription factor SOX-2
KeywordsTRANSCRIPTION / Cell reprogramming / transcription factor / DNA binding
Function / homology
Function and homology information


diencephalon morphogenesis / olfactory placode formation / lens induction in camera-type eye / ectodermal cell fate commitment / response to benzoic acid / retina morphogenesis in camera-type eye / regulation of myofibroblast cell apoptotic process / mesodermal cell fate commitment / HMG box domain binding / detection of mechanical stimulus involved in equilibrioception ...diencephalon morphogenesis / olfactory placode formation / lens induction in camera-type eye / ectodermal cell fate commitment / response to benzoic acid / retina morphogenesis in camera-type eye / regulation of myofibroblast cell apoptotic process / mesodermal cell fate commitment / HMG box domain binding / detection of mechanical stimulus involved in equilibrioception / pigment biosynthetic process / trophectodermal cell fate commitment / forebrain neuron differentiation / anatomical structure formation involved in morphogenesis / adenohypophysis development / blastocyst growth / response to oxygen-glucose deprivation / positive regulation of epithelial cell differentiation / regulation of asymmetric cell division / endodermal cell fate specification / Deactivation of the beta-catenin transactivating complex / negative regulation of cell cycle G1/S phase transition / endodermal cell fate commitment / germ-line stem cell population maintenance / positive regulation of cell-cell adhesion / POU domain binding / detection of mechanical stimulus involved in sensory perception of sound / negative regulation of calcium ion-dependent exocytosis / neuron fate commitment / trophectodermal cell differentiation / neuronal stem cell population maintenance / male genitalia development / response to growth factor / female germ cell nucleus / miRNA binding / cell fate specification / germ cell nucleus / tongue development / inner ear morphogenesis / epithelial tube branching involved in lung morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / positive regulation of neuroblast proliferation / negative regulation of Wnt signaling pathway / stem cell population maintenance / lung alveolus development / cytokine binding / positive regulation of Notch signaling pathway / somatic stem cell population maintenance / negative regulation of cell differentiation / blastocyst development / neuroblast proliferation / negative regulation of neuron differentiation / regulation of neurogenesis / positive regulation of transcription initiation by RNA polymerase II / anatomical structure morphogenesis / negative regulation of osteoblast differentiation / embryonic organ development / cell fate commitment / cis-regulatory region sequence-specific DNA binding / response to retinoic acid / Notch signaling pathway / cellular response to cadmium ion / positive regulation of neuron differentiation / transcription repressor complex / cellular response to leukemia inhibitory factor / male germ cell nucleus / response to organic substance / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / lysine-acetylated histone binding / cerebral cortex development / chromatin DNA binding / neuron differentiation / osteoblast differentiation / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / gene expression / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / positive regulation of MAPK cascade / transcription by RNA polymerase II / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin binding / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression
Similarity search - Function
Transcription factor SOX / SOX transcription factor / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / High mobility group box domain ...Transcription factor SOX / SOX transcription factor / POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / High mobility group box domain / DNA Binding (I), subunit A / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / lambda repressor-like DNA-binding domains / Homeobox domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / 434 Repressor (Amino-terminal Domain) / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / POU domain, class 5, transcription factor 1 / Transcription factor SOX-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.451 Å
AuthorsVahokoski, J. / Meusch, D. / Groves, M. / Pogenberg, V. / Wilmanns, M.
CitationJournal: To Be Published
Title: Oct4/Sox2:UTF1 structure
Authors: Vahokoski, J. / Pogenberg, V. / Wilmanns, M.
History
DepositionOct 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(P*CP*CP*TP*CP*AP*TP*TP*GP*TP*TP*AP*TP*GP*CP*TP*AP*GP*TP*GP*AP*AP*G)-3')
B: DNA (5'-D(*TP*TP*CP*AP*CP*TP*AP*GP*CP*AP*TP*AP*AP*CP*AP*AP*TP*GP*AP*GP*G)-3')
D: Transcription factor SOX-2
E: POU domain, class 5, transcription factor 1


Theoretical massNumber of molelcules
Total (without water)41,1374
Polymers41,1374
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-27 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.170, 165.170, 39.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: DNA chain DNA (5'-D(P*CP*CP*TP*CP*AP*TP*TP*GP*TP*TP*AP*TP*GP*CP*TP*AP*GP*TP*GP*AP*AP*G)-3')


Mass: 6757.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: DNA chain DNA (5'-D(*TP*TP*CP*AP*CP*TP*AP*GP*CP*AP*TP*AP*AP*CP*AP*AP*TP*GP*AP*GP*G)-3')


Mass: 6455.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Protein Transcription factor SOX-2


Mass: 10092.858 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sox2, Sox-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P48432
#4: Protein POU domain, class 5, transcription factor 1 / / NF-A3 / Octamer-binding protein 3 / Oct-3 / Octamer-binding protein 4 / Oct-4 / Octamer-binding ...NF-A3 / Octamer-binding protein 3 / Oct-3 / Octamer-binding protein 4 / Oct-4 / Octamer-binding transcription factor 3 / OTF-3


Mass: 17831.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pou5f1, Oct-3, Oct-4, Otf-3, Otf3 / Production host: Escherichia coli (E. coli) / References: UniProt: P20263

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM 4-morpholineethanesulfonic acid at pH 6.0, 33% v/v 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.45→48.62 Å / Num. obs: 8480 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 12.5
Reflection shellResolution: 3.45→3.6 Å / Rmerge(I) obs: 0.998

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O4X

1o4x


Resolution: 3.451→47.68 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 683 8.06 %
Rwork0.2011 --
obs0.205 8479 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.451→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 879 0 0 2287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042415
X-RAY DIFFRACTIONf_angle_d0.6473438
X-RAY DIFFRACTIONf_dihedral_angle_d21.6491313
X-RAY DIFFRACTIONf_chiral_restr0.034383
X-RAY DIFFRACTIONf_plane_restr0.003291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4515-3.71790.34851340.27431523X-RAY DIFFRACTION100
3.7179-4.09180.30471340.23311543X-RAY DIFFRACTION100
4.0918-4.68350.25311370.19521544X-RAY DIFFRACTION100
4.6835-5.8990.29121360.2081568X-RAY DIFFRACTION100
5.899-47.6850.19351420.17421618X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.3861-2.218-5.51550.95132.13875.3647-0.09121.4253-1.83313.9639-0.03890.40574.793-2.05660.29882.2741-0.0536-0.24591.34380.15812.518632.43450.53462.09
26.49222.0418-0.27824.0871-3.26155.37241.0568-0.3507-0.28250.539-0.43261.49361.60290.0744-0.66331.3794-0.02150.14610.9764-0.05831.329717.027462.57896.065
36.64412.0084-1.49759.0570.7928.6353-0.98990.5013-0.71761.9475-0.80842.12691.9573-0.35671.63311.7372-0.14660.4942.0629-0.09952.8153-11.117160.469812.9915
45.1738-4.27270.15553.73610.43131.90230.27291.5947-2.742-2.151-0.8430.97060.44430.60690.16141.8187-0.0456-0.02611.4162-0.29153.1678-10.074354.68129.7545
53.31.9095-1.54143.80880.42294.7688-0.7152-1.1942-1.67780.68270.0994-0.28861.1340.5740.53141.34710.27470.05951.26260.03441.481323.376859.14244.4679
63.84140.65680.15056.6216-0.87035.51771.41211.527-1.0291-0.2938-0.6969-1.06750.79780.978-0.66351.06260.06410.13821.0924-0.1740.953737.944665.24330.4146
77.81283.84982.74145.40355.21365.15520.43470.2434-1.78872.41820.8571-0.56570.8810.7324-0.0921.87410.2347-0.1191.10380.21330.172237.427367.290111.22
86.46193.52495.64035.05912.63475.0514-1.04781.17821.9575-0.2315-1.15060.0412-0.33810.58991.3171.07790.26260.18341.1042-0.03090.763728.747377.3869-1.9889
97.5677-0.98624.38495.1533-3.98434.86440.38441.7193-1.1176-1.80930.11251.98721.33420.1789-0.14351.02020.06990.10421.2864-0.21871.197317.679661.1913-6.226
103.8077-2.7813.05293.49860.1495.43331.49721.97780.3761-0.6779-0.69230.30210.63540.0723-0.75060.87660.1140.10411.15380.16561.12585.48176.0006-9.9153
113.9857-3.3090.11385.2493-0.54662.3547-0.0065-0.35411.12340.35960.18180.0499-0.29390.3505-0.33880.81860.04270.04360.8871-0.24111.021814.348883.86850.1838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 3 )
2X-RAY DIFFRACTION2chain 'A' and (resid 4 through 13 )
3X-RAY DIFFRACTION3chain 'A' and (resid 14 through 20 )
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 4 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 20 )
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 29 )
7X-RAY DIFFRACTION7chain 'D' and (resid 30 through 45 )
8X-RAY DIFFRACTION8chain 'D' and (resid 46 through 66 )
9X-RAY DIFFRACTION9chain 'D' and (resid 67 through 77 )
10X-RAY DIFFRACTION10chain 'E' and (resid -1 through 23 )
11X-RAY DIFFRACTION11chain 'E' and (resid 24 through 99 )

+
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