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- PDB-1cqg: HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERME... -
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Basic information
Entry | Database: PDB / ID: 1cqg | ||||||
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Title | 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 REF-1 (RESIDUES 59-71 OF THE P50 SUBUNIT OF NFKB), NMR, 31 STRUCTURES | ||||||
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![]() | COMPLEX (ELECTRON TRANSPORT/PEPTIDE) / COMPLEX / ELECTRON TRANSPORT/PEPTIDE / COMPLEX (ELECTRON TRANSPORT-PEPTIDE) COMPLEX | ||||||
Function / homology | ![]() Protein repair / Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / cellular detoxification of hydrogen peroxide / double-stranded DNA exodeoxyribonuclease activity / positive regulation of peptidyl-cysteine S-nitrosylation ...Protein repair / Resolution of Abasic Sites (AP sites) / class II DNA-(apurinic or apyrimidinic site) endonuclease activity / phosphodiesterase activity, acting on 3'-phosphoglycolate-terminated DNA strands / telomere maintenance via base-excision repair / site-specific endodeoxyribonuclease activity, specific for altered base / DNA-(abasic site) binding / cellular detoxification of hydrogen peroxide / double-stranded DNA exodeoxyribonuclease activity / positive regulation of peptidyl-cysteine S-nitrosylation / protein-disulfide reductase (NAD(P)H) activity / double-stranded telomeric DNA binding / phosphodiesterase I activity / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / positive regulation of gene expression via chromosomal CpG island demethylation / Displacement of DNA glycosylase by APEX1 / phosphoric diester hydrolase activity / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / uracil DNA N-glycosylase activity / DNA catabolic process / Regulation of FOXO transcriptional activity by acetylation / NFE2L2 regulating anti-oxidant/detoxification enzymes / 3'-5'-DNA exonuclease activity / response to nitric oxide / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / Detoxification of Reactive Oxygen Species / The NLRP3 inflammasome / protein-disulfide reductase activity / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / positive regulation of DNA binding / Purinergic signaling in leishmaniasis infection / DNA-(apurinic or apyrimidinic site) endonuclease activity / regulation of mRNA stability / 3'-5' exonuclease activity / activation of protein kinase B activity / telomere maintenance / base-excision repair, gap-filling / cell redox homeostasis / DNA endonuclease activity / TP53 Regulates Metabolic Genes / response to radiation / base-excision repair / chromatin DNA binding / transcription corepressor activity / RNA-DNA hybrid ribonuclease activity / positive regulation of peptidyl-serine phosphorylation / regulation of apoptotic process / Oxidative Stress Induced Senescence / endonuclease activity / DNA recombination / chromosome, telomeric region / damaged DNA binding / oxidoreductase activity / transcription coactivator activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / ribosome / nuclear speck / DNA repair / centrosome / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR | ||||||
![]() | Clore, G.M. / Qin, J. / Gronenborn, A.M. | ||||||
![]() | ![]() Title: The solution structure of human thioredoxin complexed with its target from Ref-1 reveals peptide chain reversal. Authors: Qin, J. / Clore, G.M. / Kennedy, W.P. / Kuszewski, J. / Gronenborn, A.M. #1: ![]() Title: Solution Structure of Human Thioredoxin in a Mixed Disulfide Intermediate Complex with its Target Peptide from the Transcription Factor NF Kappa B Authors: Qin, J. / Clore, G.M. / Kennedy, W.M. / Huth, J.R. / Gronenborn, A.M. #2: ![]() Title: The High-Resolution Three-Dimensional Solution Structures of the Oxidized and Reduced States of Human Thioredoxin Authors: Qin, J. / Clore, G.M. / Gronenborn, A.M. #3: ![]() Title: High-Resolution Three-Dimensional Structure of Reduced Recombinant Human Thioredoxin in Solution Authors: Forman-Kay, J.D. / Clore, G.M. / Wingfield, P.T. / Gronenborn, A.M. | ||||||
History |
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Structure visualization
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-Validation report
Summary document | ![]() | 354.4 KB | Display | ![]() |
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Full document | ![]() | 719.2 KB | Display | |
Data in XML | ![]() | 61.4 KB | Display | |
Data in CIF | ![]() | 108.7 KB | Display | |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 11592.125 Da / Num. of mol.: 1 / Mutation: CHAIN A, C35A, C62A, C69A, C73A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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#2: Protein/peptide | Mass: 1404.611 Da / Num. of mol.: 1 / Fragment: RESIDUES 59 - 71 OF THE P50 SUBUNIT OF NFKB Source method: isolated from a genetically manipulated source References: UniProt: P27695, DNA-(apurinic or apyrimidinic site) lyase |
Sequence details | THR AT POSITION 74 WAS FOUND BY WOLMAN ET AL., JOURNAL OF BIOCHEMIST |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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Processing
Refinement | Software ordinal: 1 Details: OTHER REFINEMENT REMARKS: THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. & ...Details: OTHER REFINEMENT REMARKS: 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. MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1994) J. MAGN. RESON SERIES B 104 99 - 103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92 - 96), AND PROTON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON SERIES B 107, 293 - 297) RESTRAINTS, AND A CONFORMATIONAL DATABASE POTENTIAL TERM (KUSZEWSKI, GRONENBORN & CLORE (1996) PROTEIN SCIENCE IN PRESS). ALL STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE. THE 3D STRUCTURE OF THE HUMAN THIOREDOXIN-NFKB PEPTIDE COMPLEX IN SOLUTION BY NMR IS BASED ON 3213 EXPERIMENTAL RESTRAINTS COMPRISING: 2581 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS 36 RESTRAINTS FOR 18 BACKBONE H-BONDS 321 TORSION ANGLE RESTRAINTS (104 PHI, 76 PSI, 78 CHI1, AND 30 CHI2 FOR HUMAN THIOREDOXIN, AND 11 PHI, 9 PSI, 9 CHI1, AND 4 CHI2 ANGLES FOR THE REF-1 PEPTIDE 86 HN-HALPHA THREE-BOND COUPLING CONSTANTS 100 13CALPHA AND 97 13CB CHEMICAL SHIFT RESTRAINTS. 442 1H CHEMICAL SHIFT RESTRAINTS (MADE UP OF 113 CAH, 67 METHYL GROUPS AND 262 OTHER NON-EXCHANGEABLE PROTONS). THE BREAKDOWN OF THE INTERPROTON DISTANCE RESTRAINTS IS AS FOLLOWS: INTRAMOLECULAR HTRX RESTRAINTS: 534 SEQUENTIAL 539 SHORT RANGE (1 < |I-J|<=5) 688 LONG RANGE (|I-J|>5) 682 INTRARESIDUE INTRAMOLECULAR PEPTIDE RESTRAINTS: 83 INTERMOLECULAR HTRX-NFKB: 55 THE STRUCTURE FOUND IN PDB ENTRY 1CQH IS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 35 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. |
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NMR ensemble | Conformers submitted total number: 35 |