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

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Basic information

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


negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / 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 ...negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / 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 / cellular response to interleukin-17 / protein-disulfide reductase (NAD(P)H) activity / 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 / Regulated proteolysis of p75NTR / negative regulation of interleukin-12 production / RIP-mediated NFkB activation via ZBP1 / CLEC7A/inflammasome pathway / thioredoxin-disulfide reductase (NADPH) activity / cellular response to dsRNA / Interconversion of nucleotide di- and triphosphates / Interleukin-1 processing / cellular response to interleukin-6 / negative regulation of protein export from nucleus / actinin binding / negative regulation of protein metabolic process / cellular response to angiotensin / Regulation of FOXO transcriptional activity by acetylation / Regulation of NFE2L2 gene expression / positive regulation of miRNA metabolic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / response to nitric oxide / 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 / positive regulation of DNA binding / cellular response to interleukin-1 / canonical NF-kappaB signal transduction / 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 / transcription coregulator activity / Activation of NF-kappaB in B cells / 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 / negative regulation of inflammatory response / CLEC7A (Dectin-1) signaling / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / FCERI mediated NF-kB activation / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Interleukin-1 signaling / cellular response to mechanical stimulus / cellular response to nicotine / specific granule lumen / positive regulation of canonical Wnt signaling pathway / SARS-CoV-1 activates/modulates innate immune responses / 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 / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / apoptotic process / chromatin binding / chromatin / Neutrophil degranulation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription
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 / Thioredoxin / 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
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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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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