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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
TitleRPT1 region of INI1/SNF5/SMARCB1_HUMAN - SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1.
ComponentsSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
KeywordsNUCLEAR PROTEIN / RPT1 / INI1 / actin-dependent regulator
Function / homology
Function and homology information


single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / blastocyst hatching / regulation of G0 to G1 transition ...single stranded viral RNA replication via double stranded DNA intermediate / positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / nBAF complex / brahma complex / Tat protein binding / blastocyst hatching / regulation of G0 to G1 transition / hepatocyte differentiation / regulation of nucleotide-excision repair / RSC-type complex / XY body / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / nucleosome disassembly / germ cell nucleus / positive regulation of double-strand break repair / 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 MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / positive regulation of DNA-binding transcription factor activity / kinetochore / fibrillar center / RMTs methylate histone arginines / DNA integration / nuclear matrix / p53 binding / nervous system development / transcription coactivator activity / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / SWI/SNF Subunit INI1, DNA binding domain / Chromatin-remodeling complex component Sfh1/SNF5 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1
Similarity search - Domain/homology
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsGirvin, M.E. / Cahill, S.M. / Harris, R. / Cowburn, D. / Spira, M. / Wu, X. / Prakash, R. / Bernowitz, M. / Almo, S.C. / Kalpana, G.V.
CitationJournal: Nat Commun / Year: 2021
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.
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)9,5731
Polymers9,5731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6680 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 / BRG1-associated factor 47 / BAF47 / Integrase interactor 1 protein / SNF5 homolog / hSNF5


Mass: 9572.915 Da / Num. of mol.: 1 / Fragment: UNP Residues 174-256
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCB1, BAF47, INI1, SNF5L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12824

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic22D 1H-15N HSQC
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-13C HSQC aromatic
151isotropic13D HNCO
1101isotropic13D CBCA(CO)NH
191isotropic13D HNCA
181isotropic13D HN(CA)CB
171isotropic13D HNHA
161isotropic23D 1H-13C NOESY aliphatic
1161isotropic23D 1H-13C NOESY aromatic
1151isotropic23D 1H-15N NOESY
1141isotropic23D HBHA(CO)NH
1121isotropic23D (H)CCH-COSY

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Sample preparation

DetailsType: 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
SampleConc.: 400 uM / Component: Rpt1/INI1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsDetails: 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

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX9002at NYSBC

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
AnalysisCCPNchemical shift assignment
CcpNMRCCPNstructure calculation
CNSgeometry optimization
ARIAstructure calculation
XPLOR_NIHrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 3 / Details: Xplor
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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