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- PDB-462d: CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATIO... -

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Basic information

Entry
Database: PDB / ID: 462d
TitleCRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE
ComponentsRNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G) -3')
KeywordsRNA / HIV / RNA DUPLEX / MISMATCH / BULGES / MAGNESIUM BINDING
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsEnnifar, E. / Yusupov, M. / Walter, P. / Marquet, R. / Ehresmann, C. / Ehresmann, B. / Dumas, P.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges.
Authors: Ennifar, E. / Yusupov, M. / Walter, P. / Marquet, R. / Ehresmann, B. / Ehresmann, C. / Dumas, P.
History
DepositionMar 18, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,99910
Polymers14,8052
Non-polymers1948
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.100, 59.100, 64.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

21A-557-

HOH

31A-635-

HOH

41B-585-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9998, 0.0196, 0.0093), (-0.006, -0.6622, 0.7493), (0.0209, 0.749, 0.6622)
Vector: 127.6, 7.4, -4.6)

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Components

#1: RNA chain RNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G) -3') / HIV-1(MAL) GENOMIC RNA DIMERIZATION INITIATION SITE / DIS


Mass: 7402.472 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.18 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7
Details: DROP: CACODYLATE 25MM PH 7.0, MGCL2 5MM, KCL 150MM, MPD 1%, SPERMINE 5MM; RESERVOIR: CACODYLATE 50MM PH 7.0, MGCL2 100MM, KCL 300MM, MPD 50%, VAPOR DIFFUSION, SITTING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1CACODYLATECacodylic acid11
2MGCL211
3KCL11
4MPD11
5SPERMINE11
6CACODYLATECacodylic acid12
7MGCL212
8KCL12
9MPD12
Crystal grow
*PLUS
Temperature: 37 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlRNA1drop
2150 mM1dropKCl
320 mMNa cacodylate1drop
45 mM1dropMgCl2
510 %MPD1drop
650 mMspermine1drop
750 %MPD1reservoir
8300 mM1reservoirKCl
950 mMNa cacodylate1reservoir
10100 mM1reservoirMgCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21201
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)Wavelength
SYNCHROTRONESRF D2AM11.020, 1.5418
ROTATING ANODEENRAF-NONIUS FR59121.5418
Detector
TypeIDDetectorDateDetails
CUSTOM-MADE1CCDFeb 25, 1998
MAC Science DIP-2000B2IMAGE PLATEMar 7, 1998MIRRORS
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2MIRRORS
Radiation wavelength
IDWavelength (Å)Relative weight
11.021
21.54181
ReflectionResolution: 2.3→15 Å / Num. all: 5842 / Num. obs: 5842 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6 % / Rmerge(I) obs: 0.135 / % possible all: 98.3
Reflection
*PLUS
Highest resolution: 2.25 Å
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1942623.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: DERIVATIVE TO NATIVE SCALING AND HEAVY ATOM SEARCH DONE WITH PROGRAM LOCHVAT ( DUMAS, 1994, ACTA. CRYST. A50, 526-534, 537-546)
RfactorNum. reflection% reflectionSelection details
Rfree0.212 745 12.8 %RANDOM
Rwork0.211 ---
obs0.211 5832 98.5 %-
all-5832 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.97 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.27 Å20 Å2
2---0.29 Å20 Å2
3---0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-10 Å
Luzzati sigma a0.37 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1048 8 240 1296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d8.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 120 13.7 %
Rwork0.346 759 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA-MULTI-END.PARADNA-RNA.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg8.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.54

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