[日本語] English
万見
- PDB-1o4x: TERNARY COMPLEX OF THE DNA BINDING DOMAINS OF THE OCT1 AND SOX2 T... -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 1o4x
タイトルTERNARY COMPLEX OF THE DNA BINDING DOMAINS OF THE OCT1 AND SOX2 TRANSCRIPTION FACTORS WITH A 19MER OLIGONUCLEOTIDE FROM THE HOXB1 REGULATORY ELEMENT
要素
  • 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
キーワードTRANSCRIPTION/DNA / OCT1 / POU / POUS / POUHD / SOX2 / HMG-BOX / TRANSCRIPTION FACTORS / DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX
機能・相同性
機能・相同性情報


glial cell fate commitment / regulation of myofibroblast cell apoptotic process / Formation of the posterior neural plate / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / response to oxygen-glucose deprivation / endodermal cell fate specification / adenohypophysis development / negative regulation of cell cycle G1/S phase transition / 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 / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / response to oxygen-glucose deprivation / endodermal cell fate specification / adenohypophysis development / negative regulation of cell cycle G1/S phase transition / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Specification of the neural plate border / pituitary gland development / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / positive regulation of cell-cell adhesion / tissue regeneration / Transcriptional Regulation by MECP2 / Transcriptional regulation of pluripotent stem cells / eye development / neuronal stem cell population maintenance / Germ layer formation at gastrulation / response to growth factor / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / miRNA binding / inner ear development / somatic stem cell population maintenance / RNA polymerase II transcribes snRNA genes / negative regulation of neuron differentiation / RNA polymerase II core promoter sequence-specific DNA binding / forebrain development / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of cell differentiation / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / brain development / positive regulation of miRNA transcription / response to wounding / RNA polymerase II transcription regulator complex / neuron differentiation / osteoblast differentiation / chromatin organization / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / positive regulation of MAPK cascade / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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
類似検索 - 分子機能
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 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 / lambda repressor-like DNA-binding domains / 'Homeobox' domain profile. / Homeodomain / 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
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / POU domain, class 2, transcription factor 1 / Transcription factor SOX-2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法溶液NMR / CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS
データ登録者Clore, G.M. / Williams, D.C.
引用ジャーナル: J.Biol.Chem. / 年: 2004
タイトル: 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.
著者: Williams, D.C. / Cai, M. / Clore, G.M.
履歴
登録2003年7月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02004年1月27日Provider: repository / タイプ: Initial release
改定 1.12008年4月26日Group: Version format compliance
改定 1.22011年7月13日Group: Version format compliance
改定 1.32021年10月27日Group: Data collection / Database references / Derived calculations
カテゴリ: 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
改定 1.42023年12月27日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

-
構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

-
集合体

登録構造単位
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


分子量 (理論値)分子数
合計 (水以外)41,4474
ポリマ－41,4474
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_5551
NMR アンサンブル
データ基準
コンフォーマー数 (登録 / 計算)1 / 100REGULARIZED MEAN STRUCTURE
代表モデル

-
要素

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


分子量: 5816.767 Da / 分子数: 1 / 変異: C61A / 由来タイプ: 合成
#2: DNA鎖 5'-D(*CP*AP*TP*TP*AP*GP*CP*AP*TP*GP*AP*CP*AP*AP*AP*GP*AP*CP*A)-3'


分子量: 5830.827 Da / 分子数: 1 / 由来タイプ: 合成
#3: タンパク質 transcription factor Oct-1


分子量: 19081.643 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P14859
#4: タンパク質 Transcription factor SOX-2


分子量: 10717.653 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SOX2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P48431

-
実験情報

-
実験

実験手法: 溶液NMR
NMR実験
Conditions-IDExperiment-IDSolution-IDタイプ
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

-
試料調製

試料状態イオン強度: 10 mM SODIUM PHOSPHATE / pH: 6.5 / 温度: 303.00 K
結晶化
*PLUS
手法: other / 詳細: NMR

-
NMR測定

放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M
放射波長相対比: 1
NMRスペクトロメーター
タイプ製造業者モデル磁場強度 (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002
Bruker DRX600BrukerDRX6007503
Bruker DRX750BrukerDRX7508004
Bruker DRX800BrukerDRX8008005

-
解析

NMR software名称: X-PLOR NIH / バージョン: (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) / 開発者: SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE / 分類: 精密化
精密化手法: CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS / ソフトェア番号: 1
詳細: 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 ...詳細: 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アンサンブルコンフォーマー選択の基準: REGULARIZED MEAN STRUCTURE
計算したコンフォーマーの数: 100 / 登録したコンフォーマーの数: 1

+
万見について

-
お知らせ

-
2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

+
2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

+
2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

+
2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る