- PDB-2k27: Solution structure of Human Pax8 Paired Box Domain -
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基本情報
登録情報
データベース: PDB / ID: 2k27
タイトル
Solution structure of Human Pax8 Paired Box Domain
要素
Paired box protein Pax-8
キーワード
TRANSCRIPTION REGULATOR / Paired Domain / Pax8 / solution structure / triple frequency / 3D NMR / induced fit / Alternative splicing / Developmental protein / Differentiation / Disease mutation / DNA-binding / Nucleus / Paired box / Phosphoprotein / Polymorphism / Transcription / Transcription regulation
機能・相同性
機能・相同性情報
pronephric field specification / metanephric comma-shaped body morphogenesis / negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis / negative regulation of apoptotic process involved in metanephric collecting duct development / negative regulation of apoptotic process involved in metanephric nephron tubule development / positive regulation of metanephric DCT cell differentiation / regulation of thyroid-stimulating hormone secretion / metanephric nephron tubule formation / negative regulation of mesenchymal cell apoptotic process involved in metanephros development / pronephros development ...pronephric field specification / metanephric comma-shaped body morphogenesis / negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis / negative regulation of apoptotic process involved in metanephric collecting duct development / negative regulation of apoptotic process involved in metanephric nephron tubule development / positive regulation of metanephric DCT cell differentiation / regulation of thyroid-stimulating hormone secretion / metanephric nephron tubule formation / negative regulation of mesenchymal cell apoptotic process involved in metanephros development / pronephros development / mesenchymal to epithelial transition involved in metanephros morphogenesis / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / thyroid-stimulating hormone receptor activity / positive regulation of thyroid hormone generation / metanephric distal convoluted tubule development / metanephric epithelium development / otic vesicle development / Formation of intermediate mesoderm / urogenital system development / regulation of metanephric nephron tubule epithelial cell differentiation / cellular response to gonadotropin stimulus / metanephric S-shaped body morphogenesis / mesonephros development / sensory organ development / Formation of the nephric duct / positive regulation of branching involved in ureteric bud morphogenesis / negative regulation of cardiac muscle cell apoptotic process / ventricular septum development / inner ear morphogenesis / branching involved in ureteric bud morphogenesis / thyroid gland development / anatomical structure morphogenesis / central nervous system development / kidney development / sequence-specific double-stranded DNA binding / nervous system development / regulation of apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus 類似検索 - 分子機能
手法: 溶液NMR 詳細: Pax8 Paired Box Domain unveiled by means of 3D NMR techniques.
NMR実験
Conditions-ID
Experiment-ID
Solution-ID
タイプ
1
1
1
2D 1H-15N HSQC
1
2
1
2D 1H-13C HSQC CT
1
3
1
3DCBCA(CO)NH
1
4
1
3DC(CO)NH
1
5
1
3D HNCO
1
6
1
3D HNCA
1
7
1
3D HN(CA)CB
1
8
1
3DHN(CO)CA
1
9
1
3D (H)CCH-TOCSY
1
10
1
3D 1H-15N NOESY
1
11
1
3D 1H-13C NOESY
1
12
1
3D CBCANH
1
13
1
3DHN(COCA)CB
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試料調製
詳細
内容: 0.9 mM [U-100% 13C; U-100% 15N] Pax8 Paired Box Domain, 40 uM DSS, 50 mM sodium phosphate, 0.1 % sodium azide, 15 mM [U-100% 2H] DTT, 90% H2O/10% D2O 溶媒系: 90% H2O/10% D2O
試料
濃度 (mg/ml)
構成要素
Isotopic labeling
Solution-ID
0.9mM
Pax8PairedBoxDomain
[U-100% 13C; U-100% 15N]
1
40uM
DSS
1
50mM
sodiumphosphate
1
0.1 %
sodiumazide
1
15mM
DTT
[U-100% 2H]
1
試料状態
イオン強度: 50 / pH: 6.2 / 圧: ambient / 温度: 298.00 K
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NMR測定
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 Avance
Bruker
AVANCE
500
1
Bruker Avance 2
Bruker
Avance2
750
2
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解析
NMR software
名称
バージョン
開発者
分類
CYANA
2.1
Guntert, MumenthalerandWuthrich
構造決定
TALOS
(NMR-Pipe 3.5)
Cornilescu, DelaglioandBax
データ解析
ProcheckNMR
3.4
LaskowskiandMacArthur
構造検証
TopSpin
1.3
BrukerBiospin
collection
TopSpin
1.3
BrukerBiospin
解析
CARA
1.8.4
RochusKeller
chemicalshiftassignment
CARA
1.8.4
RochusKeller
データ解析
CARA
1.8.4
RochusKeller
peakpicking
Discover
2.98
AccelrysSoftwareInc.
精密化
AQUA
3.2
Rullmann, DoreleijersandKaptein
構造検証
WHAT IF
Vriend
構造検証
精密化
手法: molecular mechanics / ソフトェア番号: 1 詳細: Minimization was performed by means of Discover, with 200 iterations using the steep descent and 800 iterations using the conjugate gradients algorithms. c-terminal superposition is performed ...詳細: Minimization was performed by means of Discover, with 200 iterations using the steep descent and 800 iterations using the conjugate gradients algorithms. c-terminal superposition is performed between residues 87-135 and the n-terminal superposition can be performed between 29-62.
NMR constraints
NOE constraints total: 1794 / NOE intraresidue total count: 946 / NOE long range total count: 75 / NOE medium range total count: 185 / NOE sequential total count: 588 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 61 / Protein psi angle constraints total count: 62
代表構造
選択基準: lowest energy
NMRアンサンブル
コンフォーマー選択の基準: structures with the lowest energy 計算したコンフォーマーの数: 300 / 登録したコンフォーマーの数: 20 / Maximum lower distance constraint violation: -0.57 Å / Maximum upper distance constraint violation: 2.82 Å