[English] 日本語
Yorodumi
- PDB-1jm4: NMR Structure of P/CAF Bromodomain in Complex with HIV-1 Tat Peptide -

+
Open data


ID or keywords:

Loading...

-
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 / peptidyl-lysine acetylation / regulation of protein ADP-ribosylation / negative regulation of rRNA processing / regulatory region RNA binding / negative regulation of cellular respiration / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / diamine N-acetyltransferase ...viral gene expression / trans-activation response element binding / peptidyl-lysine acetylation / regulation of protein ADP-ribosylation / negative regulation of rRNA processing / regulatory region RNA binding / negative regulation of cellular respiration / protein serine/threonine phosphatase inhibitor 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 / positive regulation of attachment of mitotic spindle microtubules to kinetochore / Physiological factors / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / symbiont-mediated perturbation of host chromatin organization / symbiont-mediated suppression of host translation initiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / actomyosin / internal peptidyl-lysine acetylation / positive regulation of fatty acid biosynthetic process / histone H3 acetyltransferase activity / host cell nucleolus / cyclin-dependent protein serine/threonine kinase inhibitor activity / N-terminal peptidyl-lysine acetylation / ATAC complex / membrane hyperpolarization / actinin binding / Regulation of FOXO transcriptional activity by acetylation / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / limb development / A band / I band / NOTCH4 Intracellular Domain Regulates Transcription / SAGA complex / NOTCH3 Intracellular Domain Regulates Transcription / cellular response to parathyroid hormone stimulus / protein-lysine-acetyltransferase activity / protein acetylation / histone acetyltransferase binding / Formation of WDR5-containing histone-modifying complexes / Notch-HLH transcription pathway / Formation of paraxial mesoderm / histone acetyltransferase activity / acetyltransferase activity / regulation of RNA splicing / regulation of cell division / RNA Polymerase I Transcription Initiation / regulation of embryonic development / RNA-binding transcription regulator activity / regulation of DNA repair / 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 / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / cyclin binding / positive regulation of glycolytic process / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of neuron projection development / B-WICH complex positively regulates rRNA expression / kinetochore / Pre-NOTCH Transcription and Translation / positive regulation of protein localization to nucleus / memory / NOTCH1 Intracellular Domain Regulates Transcription / Metalloprotease DUBs / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / cellular response to insulin stimulus / positive regulation of NF-kappaB transcription factor activity / mitotic spindle / vasodilation / rhythmic process / HATs acetylate histones / heart development / cellular response to oxidative stress / DNA-binding transcription factor binding
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 / Bromodomain profile. / bromo domain / Bromodomain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more