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- PDB-3ssf: Crystal structure of RNA:DNA dodecamer corresponding to HIV-1 pol... -

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Basic information

Entry
Database: PDB / ID: 3ssf
TitleCrystal structure of RNA:DNA dodecamer corresponding to HIV-1 polypurine tract, at 1.6 A resolution.
Components
  • 5'-D(*CP*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*A)-3'
  • 5'-R(*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*GP*G)-3'
KeywordsRNA/DNA / Polypurine tract (PPT) of HIV-1 / RNA-DNA hybrid / reverse transcription / RNA-DNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDrozdzal, P. / Michalska, K. / Kierzek, R. / Lomozik, L. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of an RNA/DNA dodecamer corresponding to the HIV-1 polypurine tract at 1.6 Angstrom resolution
Authors: Drozdzal, P. / Michalska, K. / Kierzek, R. / Lomozik, L. / Jaskolski, M.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H.
Authors: Kopka, M.L. / Lavelle, L. / Han, G.W. / Ng, H.-L. / Dickerson, R.E.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of an RNA.DNA hybrid reveals intermolecular intercalation: dimer formation by base-pair swapping.
Authors: Han, G.W. / Kopka, M.L. / Langs, D. / Sawaya, M.R. / Dickerson, R.E.
#3: Journal: Embo J. / Year: 2001
Title: Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA
Authors: G Sarafianos, S. / Das, K. / Tantillo, C. / Clark Jr., A.D. / Ding, J. / Whitcomb, J.M. / Boyer, P.L. / Hughes, S.H. / Arnold, E.
History
DepositionJul 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*GP*G)-3'
B: 5'-D(*CP*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5735
Polymers7,5002
Non-polymers733
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-16 kcal/mol
Surface area4570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.904, 41.904, 57.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-73-

HOH

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Components

#1: RNA chain 5'-R(*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*GP*G)-3'


Mass: 3930.472 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*A)-3'


Mass: 3569.337 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 292 K / pH: 5.5
Details: 40% MPD, 0.04M hexamminecobalt(III) chloride, 0.02M magnesium chloride, 0.04M lithium chloride, 0.04M sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 4, 2009
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 8012 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 41.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.851 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJO

1pjo


Resolution: 1.6→15.32 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.319 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGEN ATOMS WERE ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 790 9.9 %RANDOM
Rwork0.181 ---
obs0.186 7204 99.5 %-
all-7994 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.13 Å20 Å2
2--0.25 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 497 3 76 576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021600
X-RAY DIFFRACTIONr_bond_other_d0.0110.02222
X-RAY DIFFRACTIONr_angle_refined_deg2.2583935
X-RAY DIFFRACTIONr_angle_other_deg1.7583577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0330.02262
X-RAY DIFFRACTIONr_gen_planes_other0.0090.0251
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 53 -
Rwork0.234 494 -
obs--94.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.01210.2341.3187-0.13582.03994.73940.028-0.28110.2197-0.04330.05560.32150.1066-0.1312-0.08360.0458-0.0035-0.03250.0215-0.00860.1022-0.708113.613912.0936
26.44462.27010.4938-0.54020.1638-0.4629-0.05060.441-0.20290.0665-0.0382-0.1387-0.36120.06410.08880.13820.0242-0.05320.0490.00260.0262-7.611113.1846-0.1169
3-0.31370.70320.07571.6817-0.98431.16230.1290.15620.1391-0.0440.00340.20270.15250.1452-0.13240.05060.0272-0.01170.04360.01640.0468-15.409825.9671-0.9276
41.58531.2601-2.65572.6379-1.08493.7920.11-0.0491-0.09590.0231-0.0876-0.18140.06960.0606-0.02240.03310.0447-0.00920.0665-0.01120.0134-6.376325.3311.5435
50.12130.2906-0.06374.7512-0.0916-0.88920.1171-0.0688-0.05160.1499-0.0524-0.0211-0.0087-0.0016-0.06470.08620.0183-0.0240.04180.01220.0029-12.517913.06358.3245
63.8040.94771.3796-0.2947-0.45480.9694-0.02210.0664-0.25370.04650.12320.0877-0.01930.1382-0.1010.06350.0136-0.05380.0389-0.02990.04692.20695.52449.1375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 4
2X-RAY DIFFRACTION2A5 - 8
3X-RAY DIFFRACTION3A9 - 12
4X-RAY DIFFRACTION4B13 - 16
5X-RAY DIFFRACTION5B17 - 20
6X-RAY DIFFRACTION6B21 - 24

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