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- PDB-2n3k: Human Brd4 ET domain in complex with MLV Integrase C-term -

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Basic information

Entry
Database: PDB / ID: 2n3k
TitleHuman Brd4 ET domain in complex with MLV Integrase C-term
Components
  • Bromodomain-containing protein 4
  • MLV integrase
KeywordsPROTEIN BINDING / Brd4 ET / MLV Integrase
Function / homology
Function and homology information


host cell late endosome membrane / virion assembly / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity ...host cell late endosome membrane / virion assembly / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / p53 binding / chromosome / regulation of inflammatory response / viral nucleocapsid / DNA recombination / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / structural constituent of virion / transcription coactivator activity / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / transcription cis-regulatory region binding / chromatin remodeling / symbiont entry into host cell / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / host cell plasma membrane / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / 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 / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 4 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Moloney murine leukemia virus
MethodSOLUTION NMR / simulated annealing
AuthorsCrowe, B.L. / Foster, M.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of the Brd4 ET domain bound to a C-terminal motif from gamma-retroviral integrases reveals a conserved mechanism of interaction.
Authors: Crowe, B.L. / Larue, R.C. / Yuan, C. / Hess, S. / Kvaratskhelia, M. / Foster, M.P.
History
DepositionJun 3, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: MLV integrase


Theoretical massNumber of molelcules
Total (without water)12,1512
Polymers12,1512
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-11 kcal/mol
Surface area7150 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 9993.413 Da / Num. of mol.: 1 / Fragment: Brd4 ET domain (UNP residues 600-678)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pEX-N-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60885
#2: Protein/peptide MLV integrase


Mass: 2157.545 Da / Num. of mol.: 1
Fragment: MLV integrase C-terminal EBM (UNP residues 1719-1735)
Source method: obtained synthetically / Source: (synth.) Moloney murine leukemia virus / References: UniProt: Q8UN00

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1142D 1H-15N HSQC
1232D 1H-15N HSQC
1312D 1H-15N HSQC
1412D 1H-13C HSQC aliphatic
1522D 1H-13C HSQC aliphatic
1651D 13C,15N-filtered WATERGATE 1H
1711D 13C,15N-filtered WATERGATE 1H
1813D HNCO
1913D HNCA
11013D HN(CA)CB
11113D CBCA(CO)NH
11213D HBHA(CO)NH
11313D (H)CCH-TOCSY
11413D CC(CO)NH-TOCSY
11512D 13C,15N-filtered 1H-1H COSY
11612D 13C,15N-filtered 1H-1H TOCSY
11712D 13C,15N-filtered 1H-1H NOESY
11822D 13C,15N-filtered 1H-1H COSY
11922D 13C,15N-filtered 1H-1H TOCSY
12022D 13C,15N-filtered 1H-1H NOESY
12113D 1H-15N NOESY
12213D 1H-13C NOESY aliphatic
12323D 1H-13C NOESY aliphatic
12413D 13C,15N-filtered(f1) 1H-15N(f2) NOESY
12523D 13C,15N-filtered(f1) 1H-13C(f2) NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4-0.8 mM [U-99% 13C; U-99% 15N] Brd4 ET, 0.4-0.8 mM MLV IN EBM, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
20.4-0.8 mM [U-99% 13C; U-99% 15N] Brd4 ET, 0.4-0.8 mM MLV IN EBM, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 100% D2O100% D2O
30.4-0.8 mM [U-99% 15N] Brd4 ET, 0.4-0.8 mM MLV IN EBM, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
40.4-0.8 mM [U-99% 15N] Brd4 ET, 20 mM [U-2H] TRIS, 100 mM sodium chloride, 0.002 v/v sodium azide, 0.5 mM DSS, 2 mM [U-2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
51 mM MLV IN EBM, 0.5 mM DSS, 0.002 v/v sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMBrd4 ET-1[U-99% 13C; U-99% 15N]0.4-0.81
mMMLV IN EBM-20.4-0.81
20 mMTRIS-3[U-2H]1
100 mMsodium chloride-41
0.002 v/vsodium azide-51
0.5 mMDSS-61
2 mMDTT-7[U-2H]1
mMBrd4 ET-8[U-99% 13C; U-99% 15N]0.4-0.82
mMMLV IN EBM-90.4-0.82
20 mMTRIS-10[U-2H]2
100 mMsodium chloride-112
0.002 v/vsodium azide-122
0.5 mMDSS-132
2 mMDTT-14[U-2H]2
mMBrd4 ET-15[U-99% 15N]0.4-0.83
mMMLV IN EBM-160.4-0.83
20 mMTRIS-17[U-2H]3
100 mMsodium chloride-183
0.002 v/vsodium azide-193
0.5 mMDSS-203
2 mMDTT-21[U-2H]3
mMBrd4 ET-22[U-99% 15N]0.4-0.84
20 mMTRIS-23[U-2H]4
100 mMsodium chloride-244
0.002 v/vsodium azide-254
0.5 mMDSS-264
2 mMDTT-27[U-2H]4
1 mMMLV IN EBM-285
0.5 mMDSS-295
0.002 v/vsodium azide-305
Sample conditionsIonic strength: 0.25 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance III HD UltrashieldBrukerAvance III HD Ultrashield6001
Bruker Avance III HD AscendBrukerAvance III HD Ascend7002
Bruker Avance III HDBrukerAVANCE III HD8003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJ8.1.17Johnson, One Moon Scientificdata analysis
NMRViewJ8.1.17Johnson, One Moon Scientificpeak picking
NMRViewJ8.1.17Johnson, One Moon Scientificchemical shift assignment
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOS-NCornilescu, Delaglio and Baxdata analysis
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure solution
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1276 / NOE intraresidue total count: 141 / NOE long range total count: 189 / NOE medium range total count: 398 / NOE sequential total count: 263 / Protein phi angle constraints total count: 59 / Protein psi angle constraints total count: 64
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 150 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5.133 ° / Maximum upper distance constraint violation: 0.285 Å
NMR ensemble rmsDistance rms dev: 0.022 Å / Distance rms dev error: 0.0214 Å

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