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- PDB-1p4q: Solution structure of the CITED2 transactivation domain in comple... -

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Basic information

Entry
Database: PDB / ID: 1p4q
TitleSolution structure of the CITED2 transactivation domain in complex with the p300 CH1 domain
Components
  • Cbp/p300-interacting transactivator 2
  • E1A-associated protein p300
KeywordsTRANSCRIPTION/TRANSFERASE / helix / protein-protein complex / TRANSCRIPTION-TRANSFERASE COMPLEX
Function / homology
Function and homology information


embryonic process involved in female pregnancy / cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / left/right pattern formation / pulmonary artery morphogenesis / embryonic heart tube left/right pattern formation / regulation of animal organ formation / adrenal cortex formation / nodal signaling pathway / embryonic camera-type eye morphogenesis ...embryonic process involved in female pregnancy / cranial nerve morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / left/right pattern formation / pulmonary artery morphogenesis / embryonic heart tube left/right pattern formation / regulation of animal organ formation / adrenal cortex formation / nodal signaling pathway / embryonic camera-type eye morphogenesis / sex determination / positive regulation of male gonad development / behavioral defense response / negative regulation of protein oligomerization / peptidyl-lysine propionylation / histone lactyltransferase (CoA-dependent) activity / peptidyl-lysine crotonylation / peptidyl-lysine butyrylation / histone butyryltransferase activity / swimming / endocardial cushion development / peptide butyryltransferase activity / regulation of tubulin deacetylation / histone H2B acetyltransferase activity / determination of left/right asymmetry in lateral mesoderm / positive regulation of peroxisome proliferator activated receptor signaling pathway / internal protein amino acid acetylation / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / lens morphogenesis in camera-type eye / granulocyte differentiation / protein propionyltransferase activity / left/right axis specification / NOTCH2 intracellular domain regulates transcription / positive regulation of cell-cell adhesion / thigmotaxis / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / negative regulation of cardiac muscle cell proliferation / positive regulation of TORC2 signaling / trophectodermal cell differentiation / internal peptidyl-lysine acetylation / histone H4 acetyltransferase activity / response to fluid shear stress / cellular response to L-leucine / histone H3 acetyltransferase activity / peripheral nervous system development / NFE2L2 regulating ER-stress associated genes / protein N-acetyltransferase activity / acetylation-dependent protein binding / Activation of the TFAP2 (AP-2) family of transcription factors / NFE2L2 regulating inflammation associated genes / NGF-stimulated transcription / cardiac neural crest cell development involved in heart development / N-terminal peptidyl-lysine acetylation / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / NFE2L2 regulates pentose phosphate pathway genes / STAT3 nuclear events downstream of ALK signaling / Polo-like kinase mediated events / NFE2L2 regulating MDR associated enzymes / bone morphogenesis / host-mediated activation of viral transcription / TGFBR3 expression / regulation of androgen receptor signaling pathway / regulation of mitochondrion organization / determination of left/right symmetry / 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 / Nuclear events mediated by NFE2L2 / face morphogenesis / Regulation of NFE2L2 gene expression / Regulation of gene expression by Hypoxia-inducible Factor / platelet formation / NOTCH3 Intracellular Domain Regulates Transcription / regulation of glycolytic process / TRAF6 mediated IRF7 activation / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / megakaryocyte development / protein-lysine-acetyltransferase activity / STAT family protein binding / nuclear androgen receptor binding / acyltransferase activity / protein acetylation / ventricular septum morphogenesis / histone acetyltransferase binding / LBD domain binding / Formation of paraxial mesoderm / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / acetyltransferase activity / histone acetyltransferase activity / FOXO-mediated transcription of cell death genes / PI5P Regulates TP53 Acetylation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / stimulatory C-type lectin receptor signaling pathway / fat cell differentiation / uterus development / heart looping
Similarity search - Function
Helix Hairpins - #2200 / CITED / CITED / CREB-binding Protein; Chain A / TAZ 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 ...Helix Hairpins - #2200 / CITED / CITED / CREB-binding Protein; Chain A / TAZ 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-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. / Helix Hairpins / Nuclear receptor coactivator, interlocking / Helix non-globular / Special / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain (BrD) profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone acetyltransferase p300 / Cbp/p300-interacting transactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFreedman, S.J. / Sun, Z.-Y.J. / Kung, A.L. / France, D.S. / Wagner, G. / Eck, M.J.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: Structural basis for negative regulation of hypoxia-inducible factor-1alpha by CITED2.
Authors: Freedman, S.J. / Sun, Z.Y. / Kung, A.L. / France, D.S. / Wagner, G. / Eck, M.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structural basis for recruitment of CBP/p300 by hypoxia-inducible factor-1alpha
History
DepositionApr 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: Cbp/p300-interacting transactivator 2
B: E1A-associated protein p300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4225
Polymers17,2262
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)17 / 25structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cbp/p300-interacting transactivator 2 / MSG-related protein 1 / MRG1 protein / P35srj


Mass: 5800.417 Da / Num. of mol.: 1 / Fragment: transactivation domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CITED2 OR MRG1 / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99967
#2: Protein E1A-associated protein p300 / p300


Mass: 11425.289 Da / Num. of mol.: 1 / Fragment: cysteine/histidine-rich 1 (CH1) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EP300 OR P300 / Plasmid: pACYC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q09472, histone acetyltransferase
#3: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1353D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM CITED/p300;10mM deut-MES, pH 6.0; 100mM NaCl; 0.1mM ZnSO499.9% D2O
21mM CITED/p300 U-15N;10mM deut-MES, pH 6.0; 100mM NaCl; 0.1mM ZnSO490% H2O/10% D2O
31mM CITED/p300 U-15N;10mM deut-MES, pH 6.0; 100mM NaCl; 0.1mM ZnSO499.9% D2O
41mM CITED/p300 U-15N,13C;10mM deut-MES, pH 6.0; 100mM NaCl; 0.1mM ZnSO490% H2O/10% D2O
51mM CITED/p300 U-15N,13C;10mM deut-MES, pH 6.0; 100mM NaCl; 0.1mM ZnSO499.9% D2O
61mM CITED/p300 10%13C;10mM deut-MES, pH 6.0; 100mM NaCl; 0.1mM ZnSO499.9% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionClassification
VNMR5.3collection
PROSA3.7processing
XEASY1.3.13data analysis
CYANA1.0.4structure solution
X-PLOR3.1refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 17

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