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

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Entry
Database: PDB / ID: 1mdi
TitleHIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN MUTANT HUMAN THIOREDOXIN AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN NFKB
Components
  • TARGET SITE IN HUMAN NFKB
  • THIOREDOXIN
KeywordsCOMPLEX (ELECTRON TRANSPORT/PEPTIDE) / COMPLEX (ELECTRON TRANSPORT-PEPTIDE) / COMPLEX (ELECTRON TRANSPORT-PEPTIDE) complex
Function / homology
Function and homology information


positive regulation of peptidyl-cysteine S-nitrosylation / I-kappaB/NF-kappaB complex / Protein repair / negative regulation of vitamin D biosynthetic process / positive regulation of hyaluronan biosynthetic process / cellular detoxification of hydrogen peroxide / mammary gland involution / protein-disulfide reductase [NAD(P)H] activity / antibacterial innate immune response / cellular response to interleukin-17 ...positive regulation of peptidyl-cysteine S-nitrosylation / I-kappaB/NF-kappaB complex / Protein repair / negative regulation of vitamin D biosynthetic process / positive regulation of hyaluronan biosynthetic process / cellular detoxification of hydrogen peroxide / mammary gland involution / protein-disulfide reductase [NAD(P)H] activity / antibacterial innate immune response / 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 lipid storage / negative regulation of interleukin-12 production / Regulated proteolysis of p75NTR / CLEC7A/inflammasome pathway / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / thioredoxin-disulfide reductase (NADPH) activity / Interconversion of nucleotide di- and triphosphates / negative regulation of protein export from nucleus / cellular response to interleukin-6 / positive regulation of macrophage derived foam cell differentiation / cellular response to dsRNA / actinin binding / non-canonical NF-kappaB signal transduction / Regulation of FOXO transcriptional activity by acetylation / positive regulation of miRNA metabolic process / Regulation of NFE2L2 gene expression / signal transduction involved in regulation of gene expression / positive regulation of DNA binding / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / Detoxification of Reactive Oxygen Species / TRAF6 mediated NF-kB activation / Transcriptional Regulation by VENTX / cellular response to angiotensin / protein-disulfide reductase activity / The NLRP3 inflammasome / positive regulation of cholesterol efflux / canonical NF-kappaB signal transduction / positive regulation of transcription initiation by RNA polymerase II / Purinergic signaling in leishmaniasis infection / JNK cascade / response to muscle stretch / negative regulation of cytokine production involved in inflammatory response / CD209 (DC-SIGN) signaling / NF-kB is activated and signals survival / cell redox homeostasis / protein sequestering activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / tumor necrosis factor-mediated signaling pathway / B cell receptor signaling pathway / transcription coregulator activity / TP53 Regulates Metabolic Genes / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Activation of NF-kappaB in B cells / cellular response to mechanical stimulus / TAK1-dependent IKK and NF-kappa-B activation / response to radiation / cellular response to virus / Transcriptional regulation of white adipocyte differentiation / PKMTs methylate histone lysines / cellular response to nicotine / CLEC7A (Dectin-1) signaling / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / FCERI mediated NF-kB activation / specific granule lumen / Interleukin-1 signaling / HCMV Early Events / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / secretory granule lumen / Oxidative Stress Induced Senescence / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / DNA-binding transcription factor activity / negative regulation of gene expression / apoptotic process / Neutrophil degranulation / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II
Similarity search - Function
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 ...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 / Thioredoxin / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / ig-like, plexins, transcription factors / IPT domain / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / p53-like transcription factor, DNA-binding / Thioredoxin domain profile. / Death-like domain superfamily / Thioredoxin domain / Ankyrin repeat / 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
Similarity search - Domain/homology
Thioredoxin / Nuclear factor NF-kappa-B p105 subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsClore, G.M. / Qin, J. / Gronenborn, A.M.
CitationJournal: Structure / Year: 1995
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.
History
DepositionFeb 27, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOREDOXIN
B: TARGET SITE IN HUMAN NFKB


Theoretical massNumber of molelcules
Total (without water)13,1502
Polymers13,1502
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: CIS PROLINE - PRO 75
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein THIOREDOXIN


Mass: 11592.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P10599
#2: Protein/peptide TARGET SITE IN HUMAN NFKB


Mass: 1557.755 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P19838
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAT POSITION 74 THR WAS FOUND BY WOLMAN ET AL., JOURNAL OF BIOCHEMISTRY 263, 15506 (1988).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other

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Processing

RefinementSoftware ordinal: 1
Details: 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 ...Details: 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 ensembleConformers submitted total number: 1

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