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- PDB-2lww: NMR structure of RelA-TAD/CBP-TAZ1 complex -

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Basic information

Entry
Database: PDB / ID: 2lww
TitleNMR structure of RelA-TAD/CBP-TAZ1 complex
Components
  • CREB-binding protein
  • Nuclear transcription factor RelA
KeywordsTRANSCRIPTION / NF-kappaB / p65
Function / homology
Function and homology information


SUMOylation of immune response proteins / Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Regulated proteolysis of p75NTR / Nuclear events mediated by NFE2L2 / Attenuation phase / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 ...SUMOylation of immune response proteins / Activation of the TFAP2 (AP-2) family of transcription factors / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Regulated proteolysis of p75NTR / Nuclear events mediated by NFE2L2 / Attenuation phase / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / RIP-mediated NFkB activation via ZBP1 / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / Regulation of gene expression by Hypoxia-inducible Factor / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / cAMP response element binding protein binding / TRAF6 mediated NF-kB activation / Notch-HLH transcription pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / NF-kB is activated and signals survival / PKMTs methylate histone lysines / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Downstream TCR signaling / prolactin signaling pathway / germ-line stem cell population maintenance / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / Cytoprotection by HMOX1 / positive regulation of Schwann cell differentiation / Estrogen-dependent gene expression / CD209 (DC-SIGN) signaling / peptide lactyltransferase (CoA-dependent) activity / cellular response to peptidoglycan / outer kinetochore / ankyrin repeat binding / negative regulation of interferon-beta production / postsynapse to nucleus signaling pathway / negative regulation of protein sumoylation / defense response to tumor cell / cellular response to interleukin-6 / N-terminal peptidyl-lysine acetylation / nucleotide-binding oligomerization domain containing 2 signaling pathway / actinin binding / MRF binding / response to UV-B / negative regulation of non-canonical NF-kappaB signal transduction / non-canonical NF-kappaB signal transduction / face morphogenesis / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / NF-kappaB complex / vascular endothelial growth factor signaling pathway / negative regulation of transcription by RNA polymerase I / toll-like receptor 4 signaling pathway / protein-lysine-acetyltransferase activity / positive regulation of amyloid-beta formation / cellular response to hepatocyte growth factor stimulus / response to cobalamin / phosphate ion binding / acetyltransferase activity / histone acetyltransferase activity / positive regulation of T cell receptor signaling pathway / cellular response to lipoteichoic acid / response to muramyl dipeptide / TFIIB-class transcription factor binding / histone acetyltransferase complex / general transcription initiation factor binding / cellular response to angiotensin / positive regulation of vascular endothelial growth factor production / canonical NF-kappaB signal transduction / hair follicle development / response to amino acid / neuropeptide signaling pathway / NF-kappaB binding / positive regulation of double-strand break repair via homologous recombination / RNA polymerase II core promoter sequence-specific DNA binding / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / response to mechanical stimulus / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity
Similarity search - Function
CREB-binding Protein; Chain A / TAZ domain / Transcription factor RelA (p65) / 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 ...CREB-binding Protein; Chain A / TAZ domain / Transcription factor RelA (p65) / 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 / 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. / ig-like, plexins, transcription factors / 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. / IPT domain / p53-like transcription factor, DNA-binding / Nuclear receptor coactivator, interlocking / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain (BrD) profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone lysine acetyltransferase CREBBP / Transcription factor p65 / Nuclear transcription factor RelA
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsMukherjee, S.P. / Ghosh, G. / Wright, P.E.
CitationJournal: Plos Biol. / Year: 2013
Title: Analysis of the RelA:CBP/p300 Interaction Reveals Its Involvement in NF-kappa B-Driven Transcription.
Authors: Mukherjee, S.P. / Behar, M. / Birnbaum, H.A. / Hoffmann, A. / Wright, P.E. / Ghosh, G.
History
DepositionAug 7, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CREB-binding protein
B: Nuclear transcription factor RelA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8005
Polymers18,6042
Non-polymers1963
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CREB-binding protein


Mass: 11281.177 Da / Num. of mol.: 1 / Fragment: TAZ-type 1 zinc finger residues 340-439
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crebbp, Cbp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45481, histone acetyltransferase
#2: Protein Nuclear transcription factor RelA / V-rel reticuloendotheliosis viral oncogene homolog A (Avian)


Mass: 7322.844 Da / Num. of mol.: 1 / Fragment: UNP residues 425-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rela, mCG_11759 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q548Y4, UniProt: Q04207*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HNCA
1313D HN(CA)CB
1423D (H)CCH-COSY
1523D 1H-13C NOESY
1622D 1H-13C HSQC
1752D 1H-15N HSQC
1853D 1H-15N TOCSY
1953D 1H-15N NOESY
110212C-filtered-13C-edited NOESY-HSQC
11122D 1H-13C HSQC aromatic
11243D HNCO
11343D HNCA
11443D HN(CA)CB
11543D CBCA(CO)NH
11613D CBCA(CO)NH
11733D 1H-13C NOESY
11833D (H)CCH-COSY
11963D 1H-15N NOESY
12063D 1H-15N TOCSY
121312C-filtered-13C-edited NOESY-HSQC
12252D 1H-15N HSQC
12362D 1H-15N HSQC
12432D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.1 mM [U-13C; U-15N] TAZ1, 1.2-1.5 mM RelA-TA2, 2 mM DTT, 20 mM TRIS, 40 mM sodium chloride, 5 % [U-2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
20.8-1.1 mM [U-13C] TAZ1, 1.2-1.5 mM RelA-TA2, 2 mM [U-2H] DTT, 20 mM [U-2H] TRIS, 40 mM sodium chloride, 99.8 % [U-2H] D2O, 100% D2O100% D2O
30.7-0.9 mM [U-13C] RelA-TA2, 1.5-1.8 mM TAZ1, 2 mM [U-2H] DTT, 20 mM [U-2H] TRIS, 40 mM sodium chloride, 99.8 % [U-2H] D2O, 100% D2O100% D2O
40.7-0.9 mM [U-13C; U-15N] RelA-TA2, 1.5-1.8 mM TAZ1, 2 mM DTT, 20 mM TRIS, 40 mM sodium chloride, 5 % [U-2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
50.8-1.1 mM [U-15N] TAZ1, 1.2-1.5 mM RelA-TA2, 2 mM DTT, 20 mM TRIS, 40 mM sodium chloride, 5 % [U-2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
60.7-0.9 mM [U-15N] RelA-TA2, 1.5-1.8 mM TAZ1, 2 mM DTT, 20 mM TRIS, 40 mM sodium chloride, 5 % [U-2H] D2O, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMTAZ1-1[U-13C; U-15N]0.8-1.11
mMRelA-TA2-21.2-1.51
2 mMDTT-31
20 mMTRIS-41
40 mMsodium chloride-51
5 %D2O-6[U-2H]1
mMTAZ1-7[U-13C]0.8-1.12
mMRelA-TA2-81.2-1.52
2 mMDTT-9[U-2H]2
20 mMTRIS-10[U-2H]2
40 mMsodium chloride-112
99.8 %D2O-12[U-2H]2
mMRelA-TA2-13[U-13C]0.7-0.93
mMTAZ1-141.5-1.83
2 mMDTT-15[U-2H]3
20 mMTRIS-16[U-2H]3
40 mMsodium chloride-173
99.8 %D2O-18[U-2H]3
mMRelA-TA2-19[U-13C; U-15N]0.7-0.94
mMTAZ1-201.5-1.84
2 mMDTT-214
20 mMTRIS-224
40 mMsodium chloride-234
5 %D2O-24[U-2H]4
mMTAZ1-25[U-15N]0.8-1.15
mMRelA-TA2-261.2-1.55
2 mMDTT-275
20 mMTRIS-285
40 mMsodium chloride-295
5 %D2O-30[U-2H]5
mMRelA-TA2-31[U-15N]0.7-0.96
mMTAZ1-321.5-1.86
2 mMDTT-336
20 mMTRIS-346
40 mMsodium chloride-356
5 %D2O-36[U-2H]6
Sample conditionsIonic strength: 40 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2012 / NOE intraresidue total count: 684 / NOE long range total count: 186 / NOE medium range total count: 441 / NOE sequential total count: 448
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.21 Å

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