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- PDB-7jyz: Solution NMR structure and dynamics of human Brd3 ET in complex w... -

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Basic information

Entry
Database: PDB / ID: 7jyz
TitleSolution NMR structure and dynamics of human Brd3 ET in complex with MLV IN CTD
Components
  • Bromodomain-containing protein 3
  • Integrase
KeywordsSIGNALING PROTEIN / Integrase / Brd3 ET / MLV IN CTD
Function / homology
Function and homology information


histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / host cell late endosome membrane / : / histone H3K9me2/3 reader activity / virion assembly / lncRNA binding / endodermal cell differentiation / protein localization to chromatin ...histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / host cell late endosome membrane / : / histone H3K9me2/3 reader activity / virion assembly / lncRNA binding / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / histone binding / DNA recombination / structural constituent of virion / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / chromatin remodeling / symbiont-mediated suppression of host gene expression / protein serine/threonine kinase activity / chromatin binding / symbiont entry into host cell / 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
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 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Bromodomain, conserved site / Bromodomain signature. / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 3 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAiyer, S. / Liu, G. / Swapna, G.V.T. / Hao, J. / Ma, L.C. / Roth, M.J. / 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
DepositionSep 1, 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: Database references / Other / Category: pdbx_database_status / struct_ref
Item: _pdbx_database_status.status_code_nmr_data / _struct_ref.pdbx_seq_one_letter_code
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: Integrase
B: Bromodomain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)21,3962
Polymers21,3962
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, T1, T2 relaxation experiments and rotational correlation times indicate the complex formation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1530 Å2
ΔGint-8 kcal/mol
Surface area14790 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Integrase


Mass: 10131.592 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Gene: gag-pro-pol / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8UN00, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: Protein Bromodomain-containing protein 3 / RING3-like protein


Mass: 11264.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15059

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC
131isotropic22D 1H-15N HSQC-TROSY
141isotropic23D HNCO
151isotropic23D HNCA
1111isotropic23D HN(CO)CA
1101isotropic23D HN(CA)CB
191isotropic23D CBCA(CO)NH
181isotropic23D HBHA(CO)NH
171isotropic23D HNHA
161isotropic23D (H)CCH-COSY
1151isotropic23D (H)CCH-TOCSY
1141isotropic23D 13C-15N simNOESY
1131isotropic23D 13C-NOESY-aromatic
2122isotropic12D 15N-T1-relaxation
2162isotropic12D 15N-T2-relaxation
2172isotropic12D HNOE

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.25 mM [U-100% 13C; U-100% 15N] Brd3 ET, 0.25 mM [U-100% 13C; U-100% 15N] MLV-IN-CTD, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O100 mM NaCl, 20mM Sodium Phosphate, 2 mM 2-mercaptoethanol13C_15N_Brd3ET_13C_15N_MLV-IN-CTD90% H2O/10% D2O
solution20.25 mM [U-15N] Brd3 ET, 0.25 mM [U-15N] MLV-IN-CTD, 20 mM sodium phosphate, 100 mM sodium chloride, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O100 mM NaCl, 20mM Sodium Phosphate, 2 mM 2-mercaptoethanol15N_Brd3ET_15N_MLV-IN-CTD90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.25 mMBrd3 ET[U-100% 13C; U-100% 15N]1
0.25 mMMLV-IN-CTD[U-100% 13C; U-100% 15N]1
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
2 mM2-mercaptoethanolnatural abundance1
0.25 mMBrd3 ET[U-15N]2
0.25 mMMLV-IN-CTD[U-15N]2
20 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
2 mM2-mercaptoethanolnatural abundance2
Sample conditions

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

Conditions-IDLabelpH
1conditions-17
2conditions-27.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD6001Equipped with 5mm TCI probe
Bruker AVANCEBrukerAVANCE8002Equipped with a 5 mm TXI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.3b, 3.2Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddarddata analysis
AutoAssign2.4Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
I-PINELee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markleychemical shift assignment
ASDP2.3Huang, Y. et al.geometry optimization
ASDP2.3Huang, Y. et al.structure calculation
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 10
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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