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- PDB-2lxt: Allosteric communication in the KIX domain proceeds through dynam... -

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Basic information

Entry
Database: PDB / ID: 2lxt
TitleAllosteric communication in the KIX domain proceeds through dynamic re-packing of the hydrophobic core
Components
  • CREB-binding protein
  • Cyclic AMP-responsive element-binding protein 1
  • Histone-lysine N-methyltransferase MLL
KeywordsTRANSFERASE/PROTEIN BINDING / CREB binding protein / mixed-lineage leukemia activation domain / phosphorylated kinase inducible domain / CREB / ternary complex / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


ATF4-CREB1 transcription factor complex / cAMP response element binding / secretory granule organization / lung saccule development / positive regulation of cardiac muscle tissue development / MECP2 regulates transcription of neuronal ligands / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / PKA-mediated phosphorylation of CREB / CREB phosphorylation / pituitary gland development ...ATF4-CREB1 transcription factor complex / cAMP response element binding / secretory granule organization / lung saccule development / positive regulation of cardiac muscle tissue development / MECP2 regulates transcription of neuronal ligands / CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling / PKA-mediated phosphorylation of CREB / CREB phosphorylation / pituitary gland development / regulation of testosterone biosynthetic process / AKT phosphorylates targets in the nucleus / NOTCH2 intracellular domain regulates transcription / protein-cysteine methyltransferase activity / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / response to potassium ion / response to purine-containing compound / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / peptide lactyltransferase (CoA-dependent) activity / hormone secretion / negative regulation of transcription by competitive promoter binding / negative regulation of DNA methylation-dependent heterochromatin formation / positive regulation of hormone secretion / NFE2L2 regulating ER-stress associated genes / peptide N-acetyltransferase activity / Gastrin-CREB signalling pathway via PKC and MAPK / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / T-helper 2 cell differentiation / regulation of short-term neuronal synaptic plasticity / positive regulation of multicellular organism growth / histone H3K18 acetyltransferase activity / regulation of smoothened signaling pathway / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / definitive hemopoiesis / NFE2L2 regulating MDR associated enzymes / positive regulation of osteoclast differentiation / MRF binding / histone H3K4 methyltransferase activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / MECP2 regulates transcription factors / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / response to glucagon / RUNX3 regulates NOTCH signaling / Regulation of gene expression by Hypoxia-inducible Factor / Nuclear events mediated by NFE2L2 / NOTCH4 Intracellular Domain Regulates Transcription / embryonic hemopoiesis / Regulation of NFE2L2 gene expression / negative regulation of transcription by RNA polymerase I / cellular response to zinc ion / anterior/posterior pattern specification / exploration behavior / NOTCH3 Intracellular Domain Regulates Transcription / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CREB1 phosphorylation through the activation of Adenylate Cyclase / TRAF6 mediated IRF7 activation / FOXO-mediated transcription of cell death genes / peptide-lysine-N-acetyltransferase activity / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / CaMK IV-mediated phosphorylation of CREB / histone methyltransferase complex / embryonic digit morphogenesis / regulation of cell size / cellular response to hepatocyte growth factor stimulus / type I pneumocyte differentiation / homeostatic process / protein acetylation / Notch-HLH transcription pathway / Formation of WDR5-containing histone-modifying complexes / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / stimulatory C-type lectin receptor signaling pathway / acetyltransferase activity / Constitutive Signaling by AKT1 E17K in Cancer / Regulation of MITF-M-dependent genes involved in pigmentation / Zygotic genome activation (ZGA) / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / MLL1 complex / Regulation of MECP2 expression and activity / histone acetyltransferase complex / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Attenuation phase / positive regulation of fat cell differentiation / positive regulation of double-strand break repair via homologous recombination / cellular response to nutrient levels / Transcriptional and post-translational regulation of MITF-M expression and activity / canonical NF-kappaB signal transduction / positive regulation of lipid biosynthetic process / histone acetyltransferase activity
Similarity search - Function
cAMP response element binding (CREB) protein / Coactivator CBP, pKID / pKID domain / KID domain profile. / Coactivator CBP, KIX domain / bZIP transcription factor / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 ...cAMP response element binding (CREB) protein / Coactivator CBP, pKID / pKID domain / KID domain profile. / Coactivator CBP, KIX domain / bZIP transcription factor / KMT2A, ePHD domain / KMT2A, PHD domain 1 / KMT2A, PHD domain 2 / KMT2A, PHD domain 3 / Methyltransferase, trithorax / : / FY-rich, N-terminal / F/Y-rich N-terminus / PHD-like zinc-binding domain / FYR domain FYRN motif profile. / "FY-rich" domain, N-terminal region / FY-rich, C-terminal / F/Y rich C-terminus / FYR domain FYRC motif profile. / "FY-rich" domain, C-terminal region / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / Cysteine-rich motif following a subset of SET domains / 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 / 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. / Post-SET domain / Post-SET domain profile. / Basic-leucine zipper (bZIP) domain signature. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Serum Albumin; Chain A, Domain 1 / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / SET domain superfamily / SET domain profile. / SET domain / Nuclear receptor coactivator, interlocking / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cyclic AMP-responsive element-binding protein 1 / Histone-lysine N-methyltransferase 2A / CREB-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsBruschweiler, S. / Schanda, P. / Konrat, R. / Tollinger, M.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Allosteric communication in the KIX domain proceeds through dynamic repacking of the hydrophobic core.
Authors: Bruschweiler, S. / Konrat, R. / Tollinger, M.
History
DepositionAug 31, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
B: Histone-lysine N-methyltransferase MLL
C: Cyclic AMP-responsive element-binding protein 1


Theoretical massNumber of molelcules
Total (without water)16,3593
Polymers16,3593
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CREB-binding protein


Mass: 10353.856 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 587-673
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP, CBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q92793, histone acetyltransferase
#2: Protein/peptide Histone-lysine N-methyltransferase MLL / ALL-1 / CXXC-type zinc finger protein 7 / Lysine N-methyltransferase 2A / KMT2A / Trithorax-like ...ALL-1 / CXXC-type zinc finger protein 7 / Lysine N-methyltransferase 2A / KMT2A / Trithorax-like protein / Zinc finger protein HRX / MLL cleavage product N320 / N-terminal cleavage product of 320 kDa / p320 / MLL cleavage product C180 / C-terminal cleavage product of 180 kDa / p180


Mass: 2061.336 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2840-2858 / Mutation: C841A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLL, ALL1, CXXC7, HRX, HTRX, KMT2A, MLL1, TRX1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q03164, histone-lysine N-methyltransferase
#3: Protein/peptide Cyclic AMP-responsive element-binding protein 1 / CREB-1 / cAMP-responsive element-binding protein 1


Mass: 3944.288 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 116-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P16220
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CO)CA
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D 1H-15N NOESY
1813D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] entity_1-1, 2 mM entity_2-2, 2 mM [U-100% 13C; U-100% 15N] entity_3-3, 25 mM sodium chloride-4, 50 mM potassium phosphate-5, 1 mM sodium azide-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-100% 13C; U-100% 15N]1
2 mMentity_2-21
2 mMentity_3-3[U-100% 13C; U-100% 15N]1
25 mMsodium chloride-41
50 mMpotassium phosphate-51
1 mMsodium azide-61
Sample conditionspH: 5.8 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3.1Linge, O'Donoghue and Nilgesstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 934 / NOE intraresidue total count: 475 / NOE long range total count: 100 / NOE medium range total count: 92 / NOE sequential total count: 267
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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