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- PDB-1qd3: HIV-1 TAR RNA/NEOMYCIN B COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qd3
TitleHIV-1 TAR RNA/NEOMYCIN B COMPLEX
ComponentsHIV-1 TAR RNA
KeywordsRNA / HIV-1 / AMINOGLYCOSIDE-RNA-COMPLEX / MINOR GROOVE BINDING
Function / homology2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose / 2-DEOXYSTREPTAMINE / RNA / RNA (> 10)
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / molecular dynamics
AuthorsFaber, C. / Sticht, H. / Roesch, P.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Structural rearrangements of HIV-1 Tat-responsive RNA upon binding of neomycin B.
Authors: Faber, C. / Sticht, H. / Schweimer, K. / Rosch, P.
#1: Journal: Biochemistry / Year: 1998
Title: Binding of Neomycin to the Tar Element of HIV-1 RNA Induces Dissociation of Tat Protein by an Allosteric Mechanism
Authors: Wang, S. / Huber, P.W. / Mei, C. / Czarnik, A.W. / Mei, H.Y.
History
DepositionJul 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 TAR RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9594
Polymers9,3091
Non-polymers6513
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)17 / 100LOWEST ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Representative

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Components

#1: RNA chain HIV-1 TAR RNA


Mass: 9308.538 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-45 / Source method: isolated from a natural source
Details: NEOMYCIN B (RESIDUES BDG-CYY-RYB-IDG) COMPLEXED IN THE RNA MINOR GROOVE
Source: (natural) Human immunodeficiency virus 1 / Genus: Lentivirus / Cell line: Z2/CDC-Z34 ISOLATE
#2: Polysaccharide 2,6-diamino-2,6-dideoxy-beta-L-idopyranose-(1-3)-alpha-D-ribofuranose


Type: oligosaccharide / Mass: 310.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a222h-1a_1-4][a2121h-1b_1-5_2*N_6*N]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Ribf]{[(3+1)][b-L-IdopN6N]{}}LINUCSPDB-CARE
#3: Sugar ChemComp-BDG / 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose / O-2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSE / 2,6-diamino-2,6-dideoxy-alpha-D-glucose / 2,6-diamino-2,6-dideoxy-D-glucose / 2,6-diamino-2,6-dideoxy-glucose


Type: D-saccharide, alpha linking / Mass: 178.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14N2O4
IdentifierTypeProgram
DGlcpN[6N]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-GlcpN6NIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-CYY / 2-DEOXYSTREPTAMINE


Mass: 162.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
141HSQC-NOESY
151(H)CCH-COSY
161(H)CCH-TOCSY
171XFILTERED-NOESY

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Sample preparation

DetailsContents: D2O
Sample conditionsIonic strength: 110 mM / pH: 6.4 / Pressure: 1 atm / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX600BrukerDRX6006001
Bruker DMX750BrukerDMX7507502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
NDEEstructure solution
Xndeestructure solution
XPLORstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LOWEST ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 100 / Conformers submitted total number: 17

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