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- PDB-6ax5: RPT1 region of INI1/SNF5/SMARCB1_HUMAN - SWI/SNF-related matrix-a... -
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Basic information
Entry | Database: PDB / ID: 6ax5 | ||||||
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Title | RPT1 region of INI1/SNF5/SMARCB1_HUMAN - SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1. | ||||||
![]() | SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 | ||||||
![]() | NUCLEAR PROTEIN / RPT1 / INI1 / actin-dependent regulator | ||||||
Function / homology | ![]() single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / blastocyst hatching / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / Tat protein binding / brahma complex / nBAF complex ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / positive regulation of pseudohyphal growth by positive regulation of transcription from RNA polymerase II promoter / blastocyst hatching / bBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / npBAF complex / Tat protein binding / brahma complex / nBAF complex / regulation of G0 to G1 transition / nucleosome disassembly / regulation of nucleotide-excision repair / hepatocyte differentiation / XY body / RSC-type complex / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / germ cell nucleus / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / positive regulation of cell differentiation / fibrillar center / kinetochore / RMTs methylate histone arginines / positive regulation of DNA-binding transcription factor activity / nuclear matrix / DNA integration / p53 binding / nervous system development / transcription coactivator activity / chromatin remodeling / cell cycle / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
![]() | Girvin, M.E. / Cahill, S.M. / Harris, R. / Cowburn, D. / Spira, M. / Wu, X. / Prakash, R. / Bernowitz, M. / Almo, S.C. / Kalpana, G.V. | ||||||
![]() | ![]() Title: INI1/SMARCB1 Rpt1 domain mimics TAR RNA in binding to integrase to facilitate HIV-1 replication. Authors: Updesh Dixit / Savita Bhutoria / Xuhong Wu / Liming Qiu / Menachem Spira / Sheeba Mathew / Richard Harris / Lucas J Adams / Sean Cahill / Rajiv Pathak / P Rajesh Kumar / Minh Nguyen / ...Authors: Updesh Dixit / Savita Bhutoria / Xuhong Wu / Liming Qiu / Menachem Spira / Sheeba Mathew / Richard Harris / Lucas J Adams / Sean Cahill / Rajiv Pathak / P Rajesh Kumar / Minh Nguyen / Seetharama A Acharya / Michael Brenowitz / Steven C Almo / Xiaoqin Zou / Alasdair C Steven / David Cowburn / Mark Girvin / Ganjam V Kalpana / ![]() Abstract: INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt1 domain and exhibits multifaceted role in HIV-1 replication. Determining the NMR structure of INI1-Rpt1 and modeling its interaction with ...INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt1 domain and exhibits multifaceted role in HIV-1 replication. Determining the NMR structure of INI1-Rpt1 and modeling its interaction with the IN-C-terminal domain (IN-CTD) reveal that INI1-Rpt1/IN-CTD interface residues overlap with those required for IN/RNA interaction. Mutational analyses validate our model and indicate that the same IN residues are involved in both INI1 and RNA binding. INI1-Rpt1 and TAR RNA compete with each other for IN binding with similar IC values. INI1-interaction-defective IN mutant viruses are impaired for incorporation of INI1 into virions and for particle morphogenesis. Computational modeling of IN-CTD/TAR complex indicates that the TAR interface phosphates overlap with negatively charged surface residues of INI1-Rpt1 in three-dimensional space, suggesting that INI1-Rpt1 domain structurally mimics TAR. This possible mimicry between INI1-Rpt1 and TAR explains the mechanism by which INI1/SMARCB1 influences HIV-1 late events and suggests additional strategies to inhibit HIV-1 replication. | ||||||
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Structure visualization
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PDBx/mmCIF format | ![]() | 526.7 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 457.4 KB | Display | ![]() |
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Full document | ![]() | 708.4 KB | Display | |
Data in XML | ![]() | 44.1 KB | Display | |
Data in CIF | ![]() | 62.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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Similar structure data | |
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 9572.915 Da / Num. of mol.: 1 / Fragment: UNP Residues 174-256 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution Contents: 400 uM [U-99% 13C; U-99% 15N] Rpt1/INI1, 90% H2O/10% D2O Details: 200-400 uM protein U-15N, 13C / Label: 1 / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 400 uM / Component: Rpt1/INI1 / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Details: 10 mm Na phosphate, 150 mM NaCl, 1 mM Na/EDTA, 5 mm TCEP Ionic strength: 160 mM / Ionic strength err: 3 / Label: 1 / pH: 6.8 Not defined / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 1 |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 3 / Details: Xplor | |||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |