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- PDB-1n4l: A DNA analogue of the polypurine tract of HIV-1 -

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Basic information

Entry
Database: PDB / ID: 1n4l
TitleA DNA analogue of the polypurine tract of HIV-1
Components
  • 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*G)-3'
  • 5'-D(*CP*TP*TP*TP*TP*TP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'
  • Reverse Transcriptase
KeywordsTRANSFERASE/DNA / MMLV RT / Polypurine Tract / HIV-1 / Asymmetric DNA / protein-DNA complex / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / virion assembly / protein-DNA complex / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / structural constituent of virion / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
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 ...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 / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / 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 / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCote, M.L. / Pflomm, M. / Georgiadis, M.M.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Staying Straight with A-tracts: A DNA Analog of the HIV-1 Polypurine Tract
Authors: Cote, M.L. / Pflomm, M. / Georgiadis, M.M.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Crystal Structures of an N-terminal Fragment from Moloney Murine Leukemia Virus Reverse Transcriptase Complexed with Nucleic Acid: Functional Implications for Template-primer Binding to the Fingers Domain
Authors: Najmudin, S. / Cote, M.L. / Sun, D. / Yohannan, S. / Montano, S.P. / Gu, J. / Georgiadis, M.M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Use of an N-terminal fragment from Moloney murine leukemia virus reverse transcriptase to facilitate crystallization and analysis of a pseudo-16-mer DNA molecule containing G-A mispairs
Authors: Cote, M.L. / Yohannan, S.J. / Georgiadis, M.M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of a pseudo-16-mer DNA with stacked guanines and two G-A mispairs coomplexed with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase
Authors: Cote, M. / Georgaidis, M.M.
History
DepositionOct 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 11, 2017Group: Other
Revision 1.4Feb 1, 2017Group: Structure summary
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 2, 2024Group: Advisory / Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _ndb_struct_na_base_pair.i_symmetry / _ndb_struct_na_base_pair_step.i_symmetry_1 / _ndb_struct_na_base_pair_step.i_symmetry_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*CP*TP*TP*TP*TP*TP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'
D: 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*G)-3'
A: Reverse Transcriptase


Theoretical massNumber of molelcules
Total (without water)38,7263
Polymers38,7263
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-D(*CP*TP*TP*TP*TP*TP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'
D: 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*G)-3'

B: 5'-D(*CP*TP*TP*TP*TP*TP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'
D: 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*G)-3'


Theoretical massNumber of molelcules
Total (without water)19,5834
Polymers19,5834
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)54.410, 146.222, 46.778
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

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


Mass: 4929.254 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*G)-3'


Mass: 4862.188 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Reverse Transcriptase / E.C.2.7.7.49 / MMLV RT


Mass: 28934.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: part of Pol polyprotein / Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03355, RNA-directed DNA polymerase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, NaCl, ADA, MgCl2, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1NaCl11
2MgCl211
3ADA11
4HEPES11
5PEG 400011
6NaCl12
7MgCl212
8ADA12
9HEPES12
10PEG 400012
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.4 mMprotein1drop
20.5 mMoligonucleotide1drop
38 %(w/v)PEG40001reservoir
40.05 MADA1reservoirpH6.5
55.0 mMmagnesium acetate1reservoir
61
71
81
91
101

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11081
21081
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONNSLS X2511.1123
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDFeb 2, 2002
RIGAKU RAXIS IV2IMAGE PLATEApr 5, 2001Yale mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 ChannelSINGLE WAVELENGTHMx-ray1
2Ni FilterSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11231
21.54181
ReflectionResolution: 2→50 Å / Num. all: 24798 / Num. obs: 23122 / % possible obs: 93.2 % / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 2691 / Rsym value: 0.15 / % possible all: 76.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % possible obs: 93.9 % / Rmerge(I) obs: 0.118
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 84.8 % / Mean I/σ(I) obs: 5.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D1U

1d1u


Resolution: 2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1249 5.4 %RANDOM
Rwork0.24 ---
all0.241 24798 --
obs0.241 23122 93.2 %-
Displacement parametersBiso mean: 42.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 650 0 145 2834
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.006
X-RAY DIFFRACTIONp_angle_d1.3
X-RAY DIFFRACTIONp_planar_tor23
LS refinement shellResolution: 2→2.1 Å
RfactorNum. reflection% reflection
Rfree0.245 1249 -
Rwork0.215 --
obs--76.1 %
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.3
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg23
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.1

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