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- PDB-6es5: Structure and dynamics conspire in the evolution of affinity betw... -

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Basic information

Entry
Database: PDB / ID: 6es5
TitleStructure and dynamics conspire in the evolution of affinity between intrinsically disordered proteins
Components
  • CID
  • NCBD
KeywordsDNA BINDING PROTEIN / NCBD / CID / Complex / IDP
Function / homology
Function and homology information


Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes ...Phosphorylation of CLOCK, acetylation of BMAL1 (ARNTL) at target gene promoters / The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex / peptide lactyltransferase (CoA-dependent) activity / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / Activation of the TFAP2 (AP-2) family of transcription factors / histone H3K18 acetyltransferase activity / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / NFE2L2 regulates pentose phosphate pathway genes / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / regulation of smoothened signaling pathway / NFE2L2 regulating MDR associated enzymes / MRF binding / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / Regulation of NFE2L2 gene expression / Nuclear events mediated by NFE2L2 / Regulation of gene expression by Hypoxia-inducible Factor / negative regulation of transcription by RNA polymerase I / NOTCH3 Intracellular Domain Regulates Transcription / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / embryonic digit morphogenesis / protein acetylation / Notch-HLH transcription pathway / Formation of paraxial mesoderm / acetyltransferase activity / positive regulation of transforming growth factor beta receptor signaling pathway / FOXO-mediated transcription of cell death genes / stimulatory C-type lectin receptor signaling pathway / homeostatic process / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / histone acetyltransferase activity / histone acetyltransferase complex / protein-lysine-acetyltransferase activity / canonical NF-kappaB signal transduction / cAMP/PKA signal transduction / Attenuation phase / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / histone acetyltransferase / regulation of cellular response to heat / positive regulation of double-strand break repair via homologous recombination / Regulation of lipid metabolism by PPARalpha / NPAS4 regulates expression of target genes / cellular response to nutrient levels / Transcriptional and post-translational regulation of MITF-M expression and activity / CD209 (DC-SIGN) signaling / BMAL1:CLOCK,NPAS2 activates circadian expression / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / Formation of the beta-catenin:TCF transactivating complex / chromatin DNA binding / Transcriptional regulation of white adipocyte differentiation / positive regulation of protein localization to nucleus / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / protein destabilization / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / tau protein binding / transcription coactivator binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / p53 binding / cellular response to UV / transcription corepressor activity / rhythmic process / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / protein-containing complex assembly / TRAF3-dependent IRF activation pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor binding / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / response to hypoxia / transcription coactivator activity / nuclear body / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / SARS-CoV-2 activates/modulates innate and adaptive immune responses / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II
Similarity search - Function
Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking domain / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP ...Creb-binding Protein; Chain: A / Nuclear receptor coactivator, CREB-bp-like, interlocking domain / Nuclear receptor coactivator, CREB-bp-like, interlocking / Nuclear receptor coactivator, CREB-bp-like, interlocking domain superfamily / Creb binding / Zinc finger, TAZ-type / TAZ domain superfamily / TAZ zinc finger / Zinc finger TAZ-type profile. / TAZ zinc finger, present in p300 and CBP / : / Histone acetyltransferase p300-like, PHD domain / Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChi, N.C.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Sci Adv / Year: 2018
Title: Structure and dynamics conspire in the evolution of affinity between intrinsically disordered proteins.
Authors: Jemth, P. / Karlsson, E. / Vogeli, B. / Guzovsky, B. / Andersson, E. / Hultqvist, G. / Dogan, J. / Guntert, P. / Riek, R. / Chi, C.N.
History
DepositionOct 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CID
B: NCBD


Theoretical massNumber of molelcules
Total (without water)10,4372
Polymers10,4372
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2170 Å2
ΔGint-16 kcal/mol
Surface area6570 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1target function

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Components

#1: Protein/peptide CID


Mass: 4823.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide NCBD


Mass: 5613.384 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q92793*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1TROSY
121isotropic13D HN(CA)CB
131isotropic13D 1H-1H NOESY
141isotropic1Filtered NOESY
151isotropic13JHNHA
161isotropic23JHNHA
171anisotropic13D HNCO
181isotropic1T1, T2, NOE
191isotropic33D HN(CA)CB

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Sample preparation

DetailsType: solution
Contents: 100 uM [U-100% 13C] 13C, 100 uM [U-100% 15N] 15N, 90% H2O/10% D2O
Label: NMR / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 uM13C[U-100% 13C]1
100 uM15N[U-100% 15N]1
Sample conditionsIonic strength: 150 Not defined / Label: @25 deg / pH: 6.5 / Pressure: 1 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCE IIBrukerAVANCE II7002
Bruker AVANCE IIBrukerAVANCE II9003

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Processing

NMR softwareName: CYANA / Developer: Guntert P. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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