PDB-1mdk: HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERME...

基本情報

• 登録情報: データベース: PDB / ID: 1mdk
• タイトル: HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN NFKB (RESIDUES 56-68 OF THE P50 SUBUNIT OF NFKB)

要素

• TARGET SITE IN HUMAN NFKB
• THIOREDOXINチオレドキシン

• キーワード: COMPLEX (ELECTRON TRANSPORT/PEPTIDE) / COMPLEX (ELECTRON TRANSPORT-PEPTIDE) / COMPLEX (ELECTRON TRANSPORT-PEPTIDE) complex

機能・相同性

分子機能:

negative regulation of calcidiol 1-monooxygenase activity / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / negative regulation of cholesterol transport / Protein repair / positive regulation of hyaluronan biosynthetic process / cellular detoxification of hydrogen peroxide / antibacterial innate immune response / mammary gland involution / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / negative regulation of interleukin-12 production / Regulated proteolysis of p75NTR / RIP-mediated NFkB activation via ZBP1 / CLEC7A/inflammasome pathway / thioredoxin-disulfide reductase (NADPH) activity / cellular response to dsRNA / Interconversion of nucleotide di- and triphosphates / cellular response to interleukin-6 / Interleukin-1 processing / negative regulation of protein export from nucleus / actinin binding / cellular response to angiotensin / Regulation of FOXO transcriptional activity by acetylation / Regulation of NFE2L2 gene expression / negative regulation of protein metabolic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / positive regulation of miRNA metabolic process / Detoxification of Reactive Oxygen Species / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Transcriptional Regulation by VENTX / protein-disulfide reductase activity / positive regulation of transcription initiation by RNA polymerase II / canonical NF-kappaB signal transduction / positive regulation of DNA binding / cellular response to interleukin-1 / Purinergic signaling in leishmaniasis infection / JNK cascade / response to muscle stretch / NF-kB is activated and signals survival / activation of protein kinase B activity / CD209 (DC-SIGN) signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / cell redox homeostasis / response to cytokine / TP53 Regulates Metabolic Genes / Activation of NF-kappaB in B cells / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / response to radiation / PKMTs methylate histone lysines / CLEC7A (Dectin-1) signaling / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / FCERI mediated NF-kB activation / Transcriptional regulation of white adipocyte differentiation / Interleukin-1 signaling / HCMV Early Events / cellular response to nicotine / cellular response to mechanical stimulus / specific granule lumen / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / positive regulation of peptidyl-serine phosphorylation / cellular response to tumor necrosis factor / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / secretory granule lumen / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / transcription regulator complex / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 炎症 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / 自然免疫系 / apoptotic process / chromatin binding / クロマチン / Neutrophil degranulation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription

ドメイン・相同性:

: / Nuclear factor NF-kappa-B, p105 subunit / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / チオレドキシン / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / ig-like, plexins, transcription factors / チオレドキシン / IPT domain / Thioredoxin, conserved site / Thioredoxin family active site. / p53-like transcription factor, DNA-binding / Death-like domain superfamily / Ankyrin repeat / Thioredoxin domain profile. / Thioredoxin domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Glutaredoxin / Glutaredoxin / Immunoglobulin E-set / Thioredoxin-like superfamily / Immunoglobulin-like fold / 3-Layer(aba) Sandwich / Alpha Beta

構成要素:

チオレドキシン / Nuclear factor NF-kappa-B p105 subunit

• 生物種: Homo sapiens (ヒト)
• 手法: 溶液NMR
• データ登録者: Clore, G.M. / Qin, J. / Gronenborn, A.M.
• 引用: ジャーナル: Structure / 年: 1995; タイトル: Solution structure of human thioredoxin in a mixed disulfide intermediate complex with its target peptide from the transcription factor NF kappa B.; 著者: Qin, J. / Clore, G.M. / Kennedy, W.M. / Huth, J.R. / Gronenborn, A.M.

履歴

登録	1995年2月27日	処理サイト: BNL
改定 1.0	1995年6月3日	Provider: repository / タイプ: Initial release
改定 1.1	2008年3月24日	Group: Version format compliance
改定 1.2	2011年7月13日	Group: Version format compliance
改定 1.3	2022年2月23日	Group: Database references / Derived calculations / Other カテゴリ: database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

集合体

登録構造単位

A: THIOREDOXIN

B: TARGET SITE IN HUMAN NFKB

概要:

• 13.1 kDa, 2 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	13,150	2
ポリマ－	13,150	2
非ポリマー	0	0
水	108	6

1

概要:

• 登録構造と同一
• 登録者が定義した集合体

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555	x,y,z	1

• Atom site foot note: 1: CIS PROLINE - PRO 75

NMR アンサンブル

	データ	基準
コンフォーマー数 (登録 / 計算)	30 / -
代表モデル

要素

#1: タンパク質

A THIOREDOXIN / チオレドキシン

詳細:

分子量: 11592.125 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 参照: UniProt: P10599

#2: タンパク質・ペプチド

B TARGET SITE IN HUMAN NFKB

詳細:

分子量: 1557.755 Da / 分子数: 1 / 由来タイプ: 組換発現 / 参照: UniProt: P19838

#3: 水

ChemComp-HOH / water / 水

詳細:

分子量: 18.015 Da / 分子数: 6 / 由来タイプ: 天然 / 式: H₂O

• 配列の詳細: AT POSITION 74 THR WAS FOUND BY WOLMAN ET AL., JOURNAL OF BIOCHEMISTRY 263, 15506 (1988).

実験情報

実験

• 実験: 手法: 溶液NMR

試料調製

• 結晶化: 手法: その他 / 詳細: NMR

解析

• 精密化: ソフトェア番号: 1 ; 詳細: THE 3D STRUCTURE OF THE HUMAN THIOREDOXIN-NFKB PEPTIDE COMPLEX IN SOLUTION BY NMR IS BASED ON 3213 EXPERIMENTAL RESTRAINTS COMPRISING: 2546 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS 36 RESTRAINTS FOR 18 BACKBONE H-BONDS 44 RESTRAINTS FOR 6 BOUND WATER MOLECULES 300 TORSION ANGLE RESTRAINTS (104 PHI, 76 PSI, 78 CHI1 AND 31 CHI2 FOR HUMAN THIOREDOXIN, AND 7 CHI1 AND 4 CHI2 RESTRAINTS FOR THE NFKB PEPTIDE) 88 HN-HALPHA THREE-BOND COUPLING CONSTANTS 102 13CALPHA AND 97 13CB CHEMICAL SHIFT RESTRAINTS. THE BREAKDOWN OF THE INTERPROTON DISTANCE RESTRAINTS IS AS FOLLOWS: INTRAMOLECULAR HTRX RESTRAINTS: 503 SEQUENTIAL 437 SHORT RANGE (1 < |I-J|<=5) 727 LONG RANGE (|I-J|>5) 690 INTRARESIDUE INTRAMOLECULAR PEPTIDE RESTRAINTS: 115 INTERMOLECULAR HTRX-NFKB: 74 THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & GRONENBORN, A.M. (1988) FEBS LETT 229, 317 - 324. ALL STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE. THE STRUCTURE FOUND IN PDB ENTRY 1MDI IS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 60 DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO RESIDUES 1 - 105 OF HTRX AND RESIDUES 57 - 67 OF THE PEPTIDE AND SUBJECTING THE RESULTING COORDINATES TO RESTRAINED MINIMIZATION. THE LAST NUMBER COLUMN IN THIS SET OF COORDINATES (THE B-FACTOR COLUMN IN X-RAY STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE NUMBERS IN THE LAST COLUMN OF THE INDIVIDUAL STRUCTURES HAVE NO MEANING.
• NMRアンサンブル: 登録したコンフォーマーの数: 30