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- PDB-1o4x: TERNARY COMPLEX OF THE DNA BINDING DOMAINS OF THE OCT1 AND SOX2 T... -

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Entry
Database: PDB / ID: 1o4x
TitleTERNARY COMPLEX OF THE DNA BINDING DOMAINS OF THE OCT1 AND SOX2 TRANSCRIPTION FACTORS WITH A 19MER OLIGONUCLEOTIDE FROM THE HOXB1 REGULATORY ELEMENT
Components
  • 5'-D(*CP*AP*TP*TP*AP*GP*CP*AP*TP*GP*AP*CP*AP*AP*AP*GP*AP*CP*A)-3'
  • 5'-D(*TP*GP*TP*CP*TP*TP*TP*GP*TP*CP*AP*TP*GP*CP*TP*AP*AP*TP*G)-3'
  • Transcription factor SOX-2
  • transcription factor Oct-1
KeywordsTRANSCRIPTION/DNA / OCT1 / POU / POUS / POUHD / SOX2 / HMG-BOX / TRANSCRIPTION FACTORS / DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / regulation of cysteine-type endopeptidase activity involved in apoptotic process / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / adenohypophysis development / response to oxygen-glucose deprivation / endodermal cell fate specification / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation ...glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / regulation of cysteine-type endopeptidase activity involved in apoptotic process / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / adenohypophysis development / response to oxygen-glucose deprivation / endodermal cell fate specification / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / negative regulation of cell cycle G1/S phase transition / pituitary gland development / Transcriptional Regulation by MECP2 / positive regulation of cell-cell adhesion / Transcriptional regulation of pluripotent stem cells / eye development / tissue regeneration / neuronal stem cell population maintenance / Germ layer formation at gastrulation / RNA Polymerase III Transcription Initiation From Type 3 Promoter / response to growth factor / RNA Polymerase III Abortive And Retractive Initiation / miRNA binding / somatic stem cell population maintenance / inner ear development / RNA polymerase II transcribes snRNA genes / negative regulation of neuron differentiation / anatomical structure morphogenesis / RNA polymerase II core promoter sequence-specific DNA binding / forebrain development / Deactivation of the beta-catenin transactivating complex / positive regulation of cell differentiation / negative regulation of canonical Wnt signaling pathway / osteoblast differentiation / response to wounding / positive regulation of miRNA transcription / RNA polymerase II transcription regulator complex / negative regulation of epithelial cell proliferation / chromatin organization / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / positive regulation of MAPK cascade / cell differentiation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
POU domain, class 2, transcription factor 1, C-terminal / POU domain, class 2, transcription factor 1 C-terminal / Octamer-binding transcription factor / 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 domain, class 2, transcription factor 1, C-terminal / POU domain, class 2, transcription factor 1 C-terminal / Octamer-binding transcription factor / 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 / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / POU domain, class 2, transcription factor 1 / Transcription factor SOX-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS
AuthorsClore, G.M. / Williams, D.C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Molecular basis for synergistic transcriptional activation by Oct1 and Sox2 revealed from the solution structure of the 42-kDa Oct1.Sox2.Hoxb1-DNA ternary transcription factor complex.
Authors: Williams, D.C. / Cai, M. / Clore, G.M.
History
DepositionJul 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*TP*GP*TP*CP*TP*TP*TP*GP*TP*CP*AP*TP*GP*CP*TP*AP*AP*TP*G)-3'
D: 5'-D(*CP*AP*TP*TP*AP*GP*CP*AP*TP*GP*AP*CP*AP*AP*AP*GP*AP*CP*A)-3'
A: transcription factor Oct-1
B: Transcription factor SOX-2


Theoretical massNumber of molelcules
Total (without water)41,4474
Polymers41,4474
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100REGULARIZED MEAN STRUCTURE
Representative

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Components

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


Mass: 5816.767 Da / Num. of mol.: 1 / Mutation: C61A / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*AP*TP*TP*AP*GP*CP*AP*TP*GP*AP*CP*AP*AP*AP*GP*AP*CP*A)-3'


Mass: 5830.827 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein transcription factor Oct-1


Mass: 19081.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P14859
#4: Protein Transcription factor SOX-2


Mass: 10717.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOX2 / Production host: Escherichia coli (E. coli) / References: UniProt: P48431

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN
121(2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
131(3) 3D HETERONUCLEAR SEPARATED
141FILTERED NOE EXPTS
151(4) IPAP EXPERIMENTS
161TRIPLE RESONANC FOR DIPOLAR COUPLINGS. DIPOLAR COUPLINGS WERE MEASURED IN PHAGE PF1

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Sample preparation

Sample conditionsIonic strength: 10 mM SODIUM PHOSPHATE / pH: 6.50 / Temperature: 303.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002
Bruker DRX600BrukerDRX6007503
Bruker DRX750BrukerDRX7508004
Bruker DRX800BrukerDRX8008005

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Processing

NMR softwareName: X-PLOR NIH / Version: (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) / Developer: SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE / Classification: refinement
RefinementMethod: CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302). THE TARGET FUNCTION COMPRISES TERMS FOR THE DIPOLAR ...Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302). THE TARGET FUNCTION COMPRISES TERMS FOR THE DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON. 133, 216- 221(1998)), INTERMOLECULAR NOE RESTRAINTS AND TORSION ANGLE RESTRAINTS. THE NON-BONDED TERMS INCLUDE A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-136), RADIUS OF GYRATION RESTRAINTS (KUSZEWSKI ET AL. (1999) J.AM.CHEM.SOC 121, 2337-2338) AT THE PROTEIN-PROTEIN AND PROTEIN-DNA INTERFACES, AND DATABASE TORSION ANGLE AND BASE-BASE POSITIONAL POTENTIALS OF MEAN FORCE (KUSZEWSKI ET AL. (2001) J.AM.CHEM.SOC 123, 3903-3918; CLORE & KUSZEWSKI (2003) J.AM.CHEM.SOC. 125, 1518-1525). THE STARTING COORDINATES FOR THE POUHD AND POUS DOMAINS OF OCT1 ARE TAKEN FROM THE 1.9 A RESOLUTION CRYSTAL STRUCTURE OF THE OCT1/MORE-DNA COMPLEX (1E3O) AND PLACED IN THE ORIENTATION OF THE 2.7 A RESOLUTION CRYSTAL STRUCTURE OF THE OCT1/PORE-DNA COMPLEX (1HFO) (REMENYI ET AL. (2001) MOL.CELL 8, 569-580). THE STARTING COORDINATES FOR SOX2 ARE DERIVED FROM THE NMR STRUCTURE OF THE RELATED BINARY SRY-DNA COMPLEX (1J46) (MURPHY ET AL. (2001) J.MOL.BIOL. 312, 481-499). THE STARTING COORDINATES FOR THE 19MER DNA WERE BUILT AS FOLLOWS: THE POUS AND POUHD HEMI-BINDING SITES (B.P. 11-14 AND 17-19, RESPECTIVELY) WERE DERIVED FROM THE 1.9 A RESIOLUTION STRUCTURE OF THE OCT1/MORE-DNA COMPLEX (1E3O); THE SOX2 BINDING SITE (B.P. 1-10) WAS DERIVED FROM THE NMR STRUCTURE OF THE BINARY SRY/DNA COMPLEX (1J46); AND THE INTERVENING SEQUENCES (B.P. 15-16) AND REGIONS CONTAINING SUBSTITUTIONS (B.P. 1, 4 AND 10) WERE DERIVED FROM CLASSICAL DNA. THE RESULTING MODEL WAS SUBJECTED TO REGULARIZATION. THE STRATEGY USED IN THE CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS CALCULATIONS IS AS FOLLOWS: THERE ARE 4 RIGID BODIES: (1) BACKBONE AND NON-INTERFACIAL SIDE CHAINS OF POUHD + B.P. 17-19 OF THE DNA (2) BACKBONE AND NON-INTERFACIAL SIDE CHAINS OF POUS; (3) BACKBONE AND NON-INTERFACIAL SIDE CHAINS OF SOX2 + B.P. 1-4 OF THE DNA; (4) THE AXIS OF THE DIPOLAR COUPLING ALIGNMENT TENSOR. RIGID BODIES 1-3 HAVE ROTATIONAL AND TRANSLATIONAL DEGREES OF FREEDOM, WHILE RIGID BODY 4 IS GIVEN ONLY ROTATIONAL DEGREES OF FREEDOM. THE FOLLOWING SIDE CHAINS WERE GIVEN TORSIONAL DEGREES OF FREEDOM: (1) POUHD: 10 RESIDUES AT POUHD-DNA INTERFACE (RESIDUES 107, 108, 113, 144, 147, 148, 151, 154, 155 AND 158) WITH 24 SIDE C AIN TORSION ANGLES RESTRAINED TO WITHIN A RANGE OF +/-20 DEGREES OF VALUES IN BINARY OCT1/DNA COMPLEXES (2) POUS: (A) 6 RESIDUES AT POUS/SOX2 INTERFACE (RESIDUES 14, 17, 18, 21, 26 AND 52); (B) 14 RESIDUES AT POUS/DNA INTERFACE (RESIDUES 20, 27, 41, 42, 44, 45, 46, 48, 49, 54, 58, 59, 62 AND 63) WITH 35 SIDE CHAIN TORSION ANGLES RESTRAINED TO WITHIN A RANGE OF +/-20 DEGREES OF VALUES IN BINARY OCT1/DNA COMPLEXES (3) SOX2: (A) 7 RESIDUES AT POUS/SOX2 INTERFACE (RESIDUES 59, 62, 63, 66, 67, 71, 73); (B) 18 RESIDUES AT SOX2/DNA INTERFACE (RESIDUES 4, 6, 7, 8, 9, 10, 12, 13 17, 31, 35, 43, 44, 51, 55, 76, 78, 79) WITH 35 SIDE CHAIN TORSION ANGLES RESTRAINED TO WITHIN A RANGE OF +/-20 DEGREES OF VALUES IN BINARY SRY/DNA COMPLEXES. BASE PAIRS 5-16 OF THE DNA WERE GIVEN TORSIONAL DEGREES OF FREEDOM WITH 220 LOOSE BACKBONE PHOSPHODIESTER TORSION ANGLE RESTRAINTS TO PREVENT LOCAL MIRROR IMAGES (MURPHY ET AL. (2001) J.MOL.BIOL. 312, 481-499). THE NUMBERING SYSTEM IS AS FOLLOWS: OCT1 POUS DOMAIN: 5-79 OCT1 POUHD DOMAIN: 110-163 SOX-2 HMG-BOX: 206-282 RESIDUES 1-4, 80-109, 201-205 AND 283-288 ARE DISORDERED IN SOLUTION AND THUS NOT INCLUDED IN THE COORDINATES. IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. IT IS IMPORTANT TO NOTE THAT SINCE THE BACKBONE AND NON- INTERFACIAL SIECHAINS OF THE THREE PROTEIN DOMAINS ARE TREATED AS RIGID BODIES, THESE NUMBERS DO NOT TAKE INTO ACCOUNT THE ERRORS IN THE X-RAY COORDINATES OF OCT1 OR THE NMR COORDINATES OF THE HOMOLOGOUS SRY. RESIDUE NUMBERING: THIS FOLLOWS THE NUMBERING USED PREVIOUS STRUCTURAL WORK ON THE BINARY OCT1/DNA COMPLEX (KLEMM ET AL. (1994) CELL 77, 21-32; REMENYI ET AL. MOL.CELL (2001) 8, 569-580); AND THE BINARY SRY/DNA COMPLEX (MURPHY ET AL. (2001) J.MOL.BIOL. 312, 481-499). THE SIDECHAINS OF K18, Q22, K262, R265 AND K276 ARE IN MULTIPLE CONFORMATIONS. EXPERIMENTAL NMR RESTRAINTS: RESIDUAL DIPOLAR COUPLINGS: 345 (1) SOX2: 51 NH, 39 NC', 49 CaC' (2) POUS: 39 NH, 33 NC', 34 CaC' (3) POUHD: 39 NH, 34 NC', 27 CaC' INTERMOLECULAR NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS: 67 (16, 48 AND 3 at POUS/SOX2, SOX2/DNA AND POUHD/DNA INTERFACES) TORSION ANGLE RESTRAINTS: 21 (18 AT POUS/SOX2 INTERFACE AND 3 AT SOX2/DNA INTERFACE). NH DIPOLAR COUPLING R-FACTORS TERNARY COMPLEX INDIVIDUAL DOMAINS SOX2 17.7% 16.5% POUS 16.7% 16.2% POUHD 17.7% 17.5% (THE VALUES GIVEN FOR THE INDIVIDUAL DOMAINS ARE CALCULATED USING A SEPARATED ALIGNMENT TENSOR FOR EACH DOMAIN AND ARE SIMPLY LISTED FOR REFERENCE. THE VALUES FOR THE TERNARY COMPLEX (USING THE RESTRAINED REGULARIZED MEAN COORDINATES) MAKE USE OF A SINGLE ALIGNMENT TENSOR FOR THE ENTIRE COMPLEX). NON-EXPERIMENTAL RESTRAINTS: (1) 220 LOOSE TORSION ANGLE RESTRAINTS FOR THE SUGAR-PHOSPHATE BACKBONE (2) 106 LOOSE TORSION ANGLE RESTRAINTS FOR SIDE CHAINS AT PROTEIN-DNA INTERFACES (3) 35 LOOSE DISTANCE RESTRAINTS AT THE POUS/DNA AND POUHD/DNA INTERFACES TO PRESERVE HYDROGEN BONDING INTERCATIONS AND SALT BRIDGES TO BASES AND PHOSPHATES (4) WEAK NCS RESTRAINT TO PROVIDE A TRANSLATIONAL RESTRANT BETWEEN POUS AND POUHD.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 100 / Conformers submitted total number: 1

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