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- PDB-1k9w: HIV-1(MAL) RNA Dimerization Initiation Site -

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Basic information

Entry
Database: PDB / ID: 1k9w
TitleHIV-1(MAL) RNA Dimerization Initiation Site
ComponentsHIV-1 DIS(Mal)UU RNA
KeywordsRNA / HIV / hairpin
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsEnnifar, E. / Walter, P. / Ehresmann, B. / Ehresmann, C. / Dumas, P.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site.
Authors: Ennifar, E. / Walter, P. / Ehresmann, B. / Ehresmann, C. / Dumas, P.
History
DepositionOct 31, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: HIV-1 DIS(Mal)UU RNA
B: HIV-1 DIS(Mal)UU RNA
C: HIV-1 DIS(Mal)UU RNA
D: HIV-1 DIS(Mal)UU RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5558
Polymers29,4584
Non-polymers974
Water00
1
A: HIV-1 DIS(Mal)UU RNA
B: HIV-1 DIS(Mal)UU RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8025
Polymers14,7292
Non-polymers733
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HIV-1 DIS(Mal)UU RNA
D: HIV-1 DIS(Mal)UU RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7533
Polymers14,7292
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.070, 27.320, 92.100
Angle α, β, γ (deg.)90.00, 93.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain
HIV-1 DIS(Mal)UU RNA


Mass: 7364.416 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: HIV-1(Mal) sequence with U265 and U287 mutations
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Isopropanol, magnesium chloride, spermine, cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Isopropanol11
2MgCl211
3spermine11
4cacodylate11
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
113 mM1dropMgCl2
225 mMMES1droppH5.6
315 mMsodium cacodylate1droppH7.0
47.5 %(w/v)2-propanol1drop
53.5 mMspermine1drop
60.150 mMRNA1drop
720 mM1reservoirMgCl2
850 mMMES1reservoirpH5.6
915 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. obs: 6955 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.042
Reflection shellResolution: 2.9→3.03 Å / Num. unique all: 909 / Rsym value: 0.296 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / % possible obs: 95.9 % / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 9.5

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→8 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 422155.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.265 436 8.8 %RANDOM
Rwork0.227 ---
all-5458 --
obs-4967 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.09661481 e/Å3
Displacement parametersBiso mean: 64.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.7 Å20 Å2-10.14 Å2
2---17.19 Å20 Å2
3---14.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-8 Å
Luzzati sigma a0.26 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1948 4 0 1952
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d14.7
X-RAY DIFFRACTIONc_improper_angle_d1.51
LS refinement shellResolution: 3.1→3.28 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 60 7.5 %
Rwork0.254 741 -
obs--90.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1LUC.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Rfactor obs: 0.227 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.51
LS refinement shell
*PLUS
Rfactor Rfree: 0.371 / Rfactor Rwork: 0.254

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