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- PDB-1jm4: NMR Structure of P/CAF Bromodomain in Complex with HIV-1 Tat Peptide -

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Basic information

Entry
Database: PDB / ID: 1jm4
TitleNMR Structure of P/CAF Bromodomain in Complex with HIV-1 Tat Peptide
Components
  • HIV-1 Tat Peptide
  • P300/CBP-associated Factor
KeywordsTRANSFERASE / Bromodomain / Protein-peptide Complex
Function / homology
Function and homology information


viral gene expression / trans-activation response element binding / regulatory region RNA binding / negative regulation of rRNA processing / negative regulation of cellular respiration / protein serine/threonine phosphatase inhibitor activity / histone H3K9 acetyltransferase activity / positive regulation of viral transcription / diamine N-acetyltransferase / diamine N-acetyltransferase activity ...viral gene expression / trans-activation response element binding / regulatory region RNA binding / negative regulation of rRNA processing / negative regulation of cellular respiration / protein serine/threonine phosphatase inhibitor activity / histone H3K9 acetyltransferase activity / positive regulation of viral transcription / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / A band / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / symbiont-mediated perturbation of host chromatin organization / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / symbiont-mediated suppression of host translation initiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / internal peptidyl-lysine acetylation / positive regulation of fatty acid biosynthetic process / histone H3 acetyltransferase activity / host cell nucleolus / actomyosin / cyclin-dependent protein serine/threonine kinase inhibitor activity / N-terminal peptidyl-lysine acetylation / ATAC complex / actinin binding / membrane hyperpolarization / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / Regulation of FOXO transcriptional activity by acetylation / RUNX3 regulates NOTCH signaling / I band / limb development / NOTCH4 Intracellular Domain Regulates Transcription / SAGA complex / NOTCH3 Intracellular Domain Regulates Transcription / cellular response to parathyroid hormone stimulus / protein-lysine-acetyltransferase activity / negative regulation of ferroptosis / protein acetylation / Notch-HLH transcription pathway / histone acetyltransferase binding / Formation of WDR5-containing histone-modifying complexes / Formation of paraxial mesoderm / acetyltransferase activity / regulation of RNA splicing / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of embryonic development / RNA-binding transcription regulator activity / histone acetyltransferase activity / regulation of DNA repair / histone acetyltransferase / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / cyclin binding / positive regulation of glycolytic process / gluconeogenesis / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / enzyme activator activity / positive regulation of transcription elongation by RNA polymerase II / positive regulation of NF-kappaB transcription factor activity / positive regulation of neuron projection development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / kinetochore / NOTCH1 Intracellular Domain Regulates Transcription / B-WICH complex positively regulates rRNA expression / positive regulation of protein localization to nucleus / Pre-NOTCH Transcription and Translation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / vasodilation / Metalloprotease DUBs / memory / histone deacetylase binding / cellular response to insulin stimulus / mitotic spindle / rhythmic process / HATs acetylate histones / heart development / cellular response to oxidative stress / DNA-binding transcription factor binding / Estrogen-dependent gene expression / host cell cytoplasm / transcription coactivator activity / regulation of cell cycle / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / chromatin remodeling / protein domain specific binding / negative regulation of cell population proliferation / DNA-templated transcription / centrosome / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription
Similarity search - Function
Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain ...Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein Tat / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance Geometry, Simulated Annealing
AuthorsMujtaba, S. / He, Y. / Zeng, L. / Farooq, A. / Carlson, J.E. / Ott, M. / Verdin, E. / Zhou, M.-M.
Citation
Journal: Mol.Cell / Year: 2002
Title: Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain
Authors: Mujtaba, S. / He, Y. / Zeng, L. / Farooq, A. / Carlson, J.E. / Ott, M. / Verdin, E. / Zhou, M.-M.
#1: Journal: Nature / Year: 1999
Title: Structure and Ligand of a Histone Acetyltransferase Bromodomain
Authors: Dhalluin, C. / Carlson, J.E. / Zeng, L. / He, C. / Aggarwal, A.K. / Zhou, M.-M.
History
DepositionJul 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 Tat Peptide
B: P300/CBP-associated Factor


Theoretical massNumber of molelcules
Total (without water)15,5372
Polymers15,5372
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)25 / 100Back Calculated Data Agree with Experimental NOESY Spectrum, Structures with Acceptable Covalent Geometry, Structures with Favorable Non-bond Energy, Structures with the Least Restraint Violations, Structures with the Lowest Energy
Representative

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Components

#1: Protein/peptide HIV-1 Tat Peptide


Mass: 1484.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The Peptide was Chemically Synthesized. / References: UniProt: P04610*PLUS
#2: Protein P300/CBP-associated Factor / P/CAF


Mass: 14052.226 Da / Num. of mol.: 1 / Fragment: Bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92831
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
2223D 15N-separated NOESY
1313D 13C-filtered NOESY
2423D 13C/15N-filtered NOESY
1512D ROESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM Bromodomain (U-15N)/Tat Peptide; 100 mM Phosphate Buffer of pH 6.5, 5 mM Perdeuterated DTT and 0.5 mM EDTA90% H2O/10% D2O
20.5 mM Bromodomain (U-13C,15N)/Tat Peptide; 100 mM Phosphate Buffer of pH 6.5, 5 mM Perdeuterated DTT and 0.5 mM EDTA99.5% D2O
30.5 mM Bromodomain (U-13C,15N, 75%-2H)/Tat Peptide; 100 mM Phosphate Buffer of pH 6.5, 5 mM Perdeuterated DTT and 0.5 mM EDTA90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM / pH: 6.5 / Pressure: Ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3Frank Delaglioprocessing
NMRView3.5Bruce Johbsondata analysis
X-PLOR/ARIA2Michael Nilgesstructure solution
X-PLOR 3.851Brungerrefinement
RefinementMethod: Distance Geometry, Simulated Annealing / Software ordinal: 1
Details: THE ARIA/X-PLOR PLATFORM HAS BEEN USED FOR THE NOE ASSIGNMENT
NMR ensembleConformer selection criteria: Back Calculated Data Agree with Experimental NOESY Spectrum, Structures with Acceptable Covalent Geometry, Structures with Favorable Non-bond Energy, Structures with the ...Conformer selection criteria: Back Calculated Data Agree with Experimental NOESY Spectrum, Structures with Acceptable Covalent Geometry, Structures with Favorable Non-bond Energy, Structures with the Least Restraint Violations, Structures with the Lowest Energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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