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- PDB-7jq8: Solution NMR structure of human Brd3 ET domain -

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Basic information

Entry
Database: PDB / ID: 7jq8
TitleSolution NMR structure of human Brd3 ET domain
Components
  • Bromodomain-containing protein 3
  • Integrase peptide
KeywordsSIGNALING PROTEIN / BET proteins / BRD3 / extra-terminal domain / MLV-IN TP
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / lncRNA binding / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / endodermal cell differentiation / protein localization to chromatin / lysine-acetylated histone binding ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / lncRNA binding / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / endodermal cell differentiation / protein localization to chromatin / lysine-acetylated histone binding / molecular condensate scaffold activity / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / chromatin organization / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / host cell plasma membrane / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / nucleus
Similarity search - Function
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-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 / NET domain superfamily / : / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / RNase H type-1 domain profile. / Bromodomain profile. / bromo domain / Bromodomain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Bromodomain-like superfamily / 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 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Gag-Pol polyprotein / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Moloney murine leukemia virus
MethodSOLUTION NMR / simulated annealing
AuthorsAiyer, S. / Swapna, G.V.T. / Roth, J.M. / Montelione, G.T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorNIH-MIRA R35GM122518 United States
National Institutes of Health/Office of the DirectorRO1 GM110639 United States
National Institutes of Health/Office of the DirectorGM120574 United States
CitationJournal: Structure / Year: 2021
Title: A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins.
Authors: Aiyer, S. / Swapna, G.V.T. / Ma, L.C. / Liu, G. / Hao, J. / Chalmers, G. / Jacobs, B.C. / Montelione, G.T. / Roth, M.J.
History
DepositionAug 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
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

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: Integrase peptide


Theoretical massNumber of molelcules
Total (without water)14,0772
Polymers14,0772
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, NMR rotational correlation times and Heteronuclear NOE experiments with and without the peptide indicated a complex formed between Brd3 ET and MLV CT TP
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1640 Å2
ΔGint-8 kcal/mol
Surface area9630 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bromodomain-containing protein 3 / RING3-like protein


Mass: 11264.543 Da / Num. of mol.: 1 / Fragment: NET domain, residues 554-640
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Plasmid: pET15_NESG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15059
#2: Protein/peptide Integrase peptide / IN / p46


Mass: 2812.281 Da / Num. of mol.: 1 / Fragment: C-terminal Tail, residues 1716-1738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus (isolate Shinnick)
Strain: isolate Shinnick / Gene: gag-pol / Plasmid: pET15_NESG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P03355, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11D 1H
121isotropic12D HNOE
131isotropic12D NH-HSQC
141isotropic12D CH-HSQC
151isotropic12D TROSY
161isotropic13D CBCA(CO)NH
1111isotropic13D HBHA(CO)NH
1101isotropic13D HNCA
191isotropic13D HN(CA)CB
181isotropic13D (H)CCH-TOCSY
171isotropic13D CN-simNOESY
2122isotropic11D 1H
2232isotropic12D NH HSQC
2222isotropic12D CHHSQC
2212isotropic12D CT CHHSQC
2202isotropic13D HNCO
2192isotropic13D HNCA
2182isotropic13D HN(CA)CB
2172isotropic13D CBCA(CO)NH
2162isotropic13D HBHA(CO)NH
2152isotropic13D (H)CCH-TOCSY
2142isotropic13D 12C-14N filtered NOESY
2132isotropic12D-homoNOESY-13C15Nfilter
2242isotropic12D HNOE
3253isotropic13D Aromatic -NOESY
3263isotropic13D CN simNOESY
4274isotropic11D 1H
4284isotropic12D NHHSQC
4324isotropic12D NH-TROSY
4314isotropic12D CHHSQC
4304isotropic13D HNCA
4294isotropic13D HN(CA)CB
4334isotropic13D HBHA(CO)NH
4344isotropic13D (H)CCH-TOCSY
4354isotropic13D CN simNOESY
4364isotropic13D 12C 14N NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-100% 13C; U-100% 15N] MLV IN TP, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O350 uL of the protein sample with 20 mM sodium phosphate, 100 mM NaCl and 2 mM 2-mercaptoethanol13C_15N_TP90% H2O/10% D2O
solution20.5 mM [U-100% 13C; U-100% 15N] Brd3 ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O275 uL of the protein sample with 20 mM sodium phosphate, 100 mM NaCl and 2 mM 2-mercaptoethanol13C_15N_Brd3-un_TP90% H2O/10% D2O
solution30.5 mM Brd3 ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O275 uL of the protein sample with 20 mM sodium phosphate, 100 mM NaCl and 2 mM 2-mercaptoethanol13C_15N_Brd3ET-TP90% H2O/10% D2O
solution40.5 mM Brd3 ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O275 uL of the protein sample with 20 mM sodium phosphate, 100 mM NaCl and 2 mM 2-mercaptoethanol13C_15N_Brd3ET-TP90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMLV IN TP[U-100% 13C; U-100% 15N]1
100 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
2 mM2-mercaptoethanolnatural abundance1
0.5 mMBrd3 ET[U-100% 13C; U-100% 15N]2
100 mMsodium chloridenatural abundance2
20 mMsodium phosphatenatural abundance2
2 mM2-mercaptoethanolnatural abundance2
0.5 mMBrd3 ETnatural abundance3
100 mMsodium chloridenatural abundance3
20 mMsodium phosphatenatural abundance3
2 mM2-mercaptoethanolnatural abundance3
0.5 mMBrd3 ETnatural abundance4
100 mMsodium chloridenatural abundance4
20 mMsodium phosphatenatural abundance4
2 mM2-mercaptoethanolnatural abundance4
Sample conditions

Details: 20 mM sodium phosphate, 100 mM NaCl and 2 mM 2-mercaptoethanol / Ionic strength: 100mM NaCl mM / Ionic strength err: 0.2 / pH: 7 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.05 / Temperature: 298 K / Temperature err: 0.1

Conditions-IDLabel
113C_15N_TP
213C_15N_Brd3_un-TP
313C_15N_Brd3-TP
413C_15N-TP_un_ET

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz / Details: Equipped with 5mm TXI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
SparkyGoddardpeak picking
ASDP2.3Huang, J and Montelione G.T.geometry optimization
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
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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