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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


: / transcription coactivator binding => GO:0001223 / : / DNA-binding transcription factor binding => GO:0140297 / DNA-binding transcription factor binding => GO:0140297 / SUMOylation of immune response proteins / Activation of the TFAP2 (AP-2) family of transcription factors / Regulated proteolysis of p75NTR / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation ...: / transcription coactivator binding => GO:0001223 / : / DNA-binding transcription factor binding => GO:0140297 / DNA-binding transcription factor binding => GO:0140297 / SUMOylation of immune response proteins / Activation of the TFAP2 (AP-2) family of transcription factors / Regulated proteolysis of p75NTR / Regulation of FOXO transcriptional activity by acetylation / TRAF6 mediated IRF7 activation / Nuclear events mediated by NFE2L2 / Interleukin-1 processing / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / Attenuation phase / RIP-mediated NFkB activation via ZBP1 / Regulation of gene expression by Hypoxia-inducible Factor / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / cAMP response element binding protein binding / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / TRAF6 mediated NF-kB activation / Notch-HLH transcription pathway / 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 / positive regulation of cell adhesion molecule production / FCERI mediated NF-kB activation / response to xenobiotic stimulus => GO:0009410 / germ-line stem cell population maintenance / CLEC7A (Dectin-1) signaling / positive regulation of chondrocyte differentiation / : / Interleukin-1 signaling / acetaldehyde metabolic process / Downstream TCR signaling / prolactin signaling pathway / negative regulation of viral process / Regulation of lipid metabolism by PPARalpha / NF-kappaB p50/p65 complex / chromatin => GO:0000785 / Cytoprotection by HMOX1 / positive regulation of Schwann cell differentiation / CD209 (DC-SIGN) signaling / Estrogen-dependent gene expression / peptide lactyltransferase (CoA-dependent) activity / outer kinetochore / cellular response to peptidoglycan / negative regulation of interferon-beta production / ankyrin repeat binding / negative regulation of protein sumoylation / defense response to tumor cell / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / histone H3K18 acetyltransferase activity / cellular response to interleukin-6 / N-terminal peptidyl-lysine acetylation / histone H3K27 acetyltransferase activity / response to morphine / actinin binding / MRF binding / cellular response to angiotensin / response to UV-B / peroxisome proliferator activated receptor binding / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / face morphogenesis / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of transcription by RNA polymerase I / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / peptide-lysine-N-acetyltransferase activity / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of dendritic spine development / positive regulation of miRNA metabolic process / response to cobalamin / positive regulation of T cell receptor signaling pathway / non-canonical NF-kappaB signal transduction / phosphate ion binding / SMAD binding / cellular response to lipoteichoic acid / response to muramyl dipeptide / behavioral response to cocaine / acetyltransferase activity / TFIIB-class transcription factor binding / general transcription initiation factor binding / positive regulation of double-strand break repair via homologous recombination / NF-kappaB binding / hair follicle development / histone acetyltransferase complex / positive regulation of vascular endothelial growth factor production / cellular response to vascular endothelial growth factor stimulus / neuropeptide signaling pathway / canonical NF-kappaB signal transduction / RNA polymerase II core promoter sequence-specific DNA binding
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 / 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-binding domain, present in Dystrophin, CREB-binding protein. / ig-like, plexins, transcription factors / 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 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

Downloads & links

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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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