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- PDB-1gtc: HUMAN IMMUNODEFICIENCY VIRUS-1 OKAZAKI FRAGMENT, DNA-RNA CHIMERA,... -

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Basic information

Entry
Database: PDB / ID: 1gtc
TitleHUMAN IMMUNODEFICIENCY VIRUS-1 OKAZAKI FRAGMENT, DNA-RNA CHIMERA, NMR, 11 STRUCTURES
Components
  • DNA (5'-D(*GP*CP*AP*GP*TP*GP*GP*C)-3')
  • DNA/RNA (5'-R(*GP*CP*CP*A)-D(P*CP*TP*GP*C)-3')
KeywordsDNA-RNA HYBRID / RNA:DNA CHIMERA / RNASE H / REVERSE TRANSCRIPTASE / DNA-RNA COMPLEX
Function / homologyDNA / DNA/RNA hybrid
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS
AuthorsFedoroff, O.Y. / Salazar, M. / Reid, B.R.
Citation
Journal: Biochemistry / Year: 1996
Title: Structural variation among retroviral primer-DNA junctions: solution structure of the HIV-1 (-)-strand Okazaki fragment r(gcca)d(CTGC).d(GCAGTGGC).
Authors: Fedoroff, O.Y.u. / Salazar, M. / Reid, B.R.
#1: Journal: Biochemistry / Year: 1993
Title: Sugar Conformations at Hybrid Duplex Junctions in HIV-1 and Okazaki Fragments
Authors: Salazar, M. / Champoux, J.J. / Reid, B.R.
History
DepositionJun 13, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*CP*AP*GP*TP*GP*GP*C)-3')
B: DNA/RNA (5'-R(*GP*CP*CP*A)-D(P*CP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,9192
Polymers4,9192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / -
Representative

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Components

#1: DNA chain DNA (5'-D(*GP*CP*AP*GP*TP*GP*GP*C)-3')


Mass: 2467.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / Genus: Lentivirus
#2: DNA/RNA hybrid DNA/RNA (5'-R(*GP*CP*CP*A)-D(P*CP*TP*GP*C)-3')


Mass: 2451.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human immunodeficiency virus 1 / Genus: Lentivirus

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121DQF-COSY
131E.COSY
141H-P HETCOR

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Sample preparation

Sample conditionspH: 7 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
ModelField strength (MHz)Spectrometer-ID
HOME BUILD5001
DROBNY5002
GLADDEN5003

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
DiscoverBIOSYMrefinement
Discoverstructure solution
DG-IIstructure solution
BIRDERstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformers submitted total number: 11

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