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- PDB-2mjv: Solution structures of second bromodomain of Brd4 with di-acetyla... -

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Basic information

Entry
Database: PDB / ID: 2mjv
TitleSolution structures of second bromodomain of Brd4 with di-acetylated Twist peptide
Components
  • Bromodomain-containing protein 4
  • Twist-related protein 1
KeywordsTRANSCRIPTION / tumorigenesis
Function / homology
Function and homology information


embryonic camera-type eye formation / cell proliferation involved in heart valve development / positive regulation of endocardial cushion to mesenchymal transition involved in heart valve formation / negative regulation of peroxisome proliferator activated receptor signaling pathway / cranial suture morphogenesis / negative regulation of double-strand break repair / negative regulation of skeletal muscle tissue development / positive regulation of DNA-templated transcription initiation / negative regulation of striated muscle tissue development / negative regulation of macrophage cytokine production ...embryonic camera-type eye formation / cell proliferation involved in heart valve development / positive regulation of endocardial cushion to mesenchymal transition involved in heart valve formation / negative regulation of peroxisome proliferator activated receptor signaling pathway / cranial suture morphogenesis / negative regulation of double-strand break repair / negative regulation of skeletal muscle tissue development / positive regulation of DNA-templated transcription initiation / negative regulation of striated muscle tissue development / negative regulation of macrophage cytokine production / cardiac neural crest cell migration involved in outflow tract morphogenesis / bHLH transcription factor binding / mitral valve morphogenesis / developmental process / Transcriptional regulation by RUNX2 / positive regulation of fatty acid beta-oxidation / positive regulation of transcription regulatory region DNA binding / regulation of bone mineralization / embryonic cranial skeleton morphogenesis / positive regulation of monocyte chemotactic protein-1 production / embryonic forelimb morphogenesis / aortic valve morphogenesis / outer ear morphogenesis / embryonic hindlimb morphogenesis / positive regulation of cell motility / muscle organ development / endocardial cushion morphogenesis / DNA-binding transcription repressor activity / embryonic digit morphogenesis / roof of mouth development / eyelid development in camera-type eye / E-box binding / negative regulation of cellular senescence / negative regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / negative regulation of tumor necrosis factor production / P-TEFb complex binding / negative regulation by host of viral transcription / negative regulation of osteoblast differentiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cis-regulatory region sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / positive regulation of T-helper 17 cell lineage commitment / positive regulation of epithelial to mesenchymal transition / energy homeostasis / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / ossification / negative regulation of miRNA transcription / condensed nuclear chromosome / positive regulation of epithelial cell proliferation / neural tube closure / transcription coregulator binding / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / lysine-acetylated histone binding / cellular response to growth factor stimulus / histone deacetylase binding / osteoblast differentiation / positive regulation of angiogenesis / Regulation of RUNX2 expression and activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / rhythmic process / p53 binding / chromosome / cellular response to hypoxia / regulation of inflammatory response / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / in utero embryonic development / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / Helix-loop-helix DNA-binding domain / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation ...: / Helix-loop-helix DNA-binding domain / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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
Bromodomain-containing protein 4 / Twist-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsZeng, L. / Zhou, M.
CitationJournal: Cancer Cell / Year: 2014
Title: Disrupting the Interaction of BRD4 with Diacetylated Twist Suppresses Tumorigenesis in Basal-like Breast Cancer.
Authors: Shi, J. / Wang, Y. / Zeng, L. / Wu, Y. / Deng, J. / Zhang, Q. / Lin, Y. / Li, J. / Kang, T. / Tao, M. / Rusinova, E. / Zhang, G. / Wang, C. / Zhu, H. / Yao, J. / Zeng, Y.X. / Evers, B.M. / ...Authors: Shi, J. / Wang, Y. / Zeng, L. / Wu, Y. / Deng, J. / Zhang, Q. / Lin, Y. / Li, J. / Kang, T. / Tao, M. / Rusinova, E. / Zhang, G. / Wang, C. / Zhu, H. / Yao, J. / Zeng, Y.X. / Evers, B.M. / Zhou, M.M. / Zhou, B.P.
History
DepositionJan 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Twist-related protein 1
B: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)16,1432
Polymers16,1432
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Twist-related protein 1 / Class A basic helix-loop-helix protein 38 / bHLHa38 / H-twist


Mass: 1300.465 Da / Num. of mol.: 1 / Fragment: peptide (UNP residues 68-79)
Source method: isolated from a genetically manipulated source
Source: (synth.) Homo sapiens (human) / References: UniProt: Q15672
#2: Protein Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 14842.058 Da / Num. of mol.: 1 / Fragment: bromodomain 2 (UNP residues 333-460)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / References: UniProt: O60885

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HN(CA)CB
1223D HN(COCA)CB
1323D 1H-15N NOESY
1423D 1H-15N TOCSY
1513D 1H-13C NOESY aliphatic
1613D 1H-13C NOESY aromatic
1713D 13C-edited 13C/15N-filtered NOESY aromatic
1813D 13C-edited 13C/15N-filtered NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
15 mM [U-100% 2H] DTT, 100 mM sodium phosphate, 100% D2O100% D2O
25 mM [U-100% 2H] DTT, 100 mM sodium phosphate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMDTT-1[U-100% 2H]1
100 mMsodium phosphate-21
5 mMDTT-3[U-100% 2H]2
100 mMsodium phosphate-42
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
NMRPipe7.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
NMRPipe7.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.04Johnson, One Moon Scientificpeak picking
NMRView5.04Johnson, One Moon Scientificdata analysis
NMRView5.04Johnson, One Moon Scientificchemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
TopSpin1.3Bruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, DGSA-distance geometry simulated annealing
Software ordinal: 1
NMR constraintsNOE constraints total: 3189 / NOE intraresidue total count: 1032 / NOE long range total count: 823 / NOE medium range total count: 688 / NOE sequential total count: 646 / Protein phi angle constraints total count: 79 / Protein psi angle constraints total count: 79
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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