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- PDB-8uo6: HIV-1 Rev Response Element (RRE) Stem-Loop II (SLII) -

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Basic information

Entry
Database: PDB / ID: 8uo6
TitleHIV-1 Rev Response Element (RRE) Stem-Loop II (SLII)
ComponentsHIV-1 Rev Response Element Stem-Loop II with tRNA scaffold
KeywordsRNA / Non-coding RNA / HIV / Nuclear Export / RRE / viral RNA
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHIV whole-genome vector AA1305#18 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsTipo, J. / Gottipati, K. / Choi, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI187856 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site.
Authors: Tipo, J. / Gottipati, K. / Slaton, M. / Gonzalez-Gutierrez, G. / Choi, K.H.
History
DepositionOct 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold
B: HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold


Theoretical massNumber of molelcules
Total (without water)86,6832
Polymers86,6832
Non-polymers00
Water00
1
A: HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold


Theoretical massNumber of molelcules
Total (without water)43,3421
Polymers43,3421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold


Theoretical massNumber of molelcules
Total (without water)43,3421
Polymers43,3421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.782, 81.314, 81.372
Angle α, β, γ (deg.)90.000, 99.140, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: A / End label comp-ID: A / Auth seq-ID: 1 - 7 / Label seq-ID: 1 - 7

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.747372200546, 0.10026959512, -0.65679586033), (-0.0763694275933, -0.994959043273, -0.0649939438615), (-0.660001897255, 0.00158445705313, 0.751262261208)Vector: 22. ...NCS oper: (Code: given
Matrix: (-0.747372200546, 0.10026959512, -0.65679586033), (-0.0763694275933, -0.994959043273, -0.0649939438615), (-0.660001897255, 0.00158445705313, 0.751262261208)
Vector: 22.6737929428, 2.59151013292, -3.31835187928)

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Components

#1: RNA chain HIV-1 Rev Response Element Stem-Loop II with tRNA scaffold


Mass: 43341.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 52_53insG
Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others)
Production host: Escherichia coli (E. coli)

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM SPG (mixture of succinic acid, sodium dihydrogen phosphate, and glycine in a 2:7:7 molar ratio), 20-24% polyethylene glycol-6000, and 200 mM sodium fluoride
PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→57.2 Å / Num. obs: 12674 / % possible obs: 88.5 % / Redundancy: 4 % / Biso Wilson estimate: 66.82 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.05 / Rrim(I) all: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 2.85→3.2 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 635 / CC1/2: 0.487 / Rpim(I) all: 0.72

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata scaling
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→57.15 Å / SU ML: 0.3332 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 605 4.78 %
Rwork0.2314 12061 -
obs0.2326 12666 61.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.73 Å2
Refinement stepCycle: LAST / Resolution: 2.85→57.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5742 0 0 5742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00266420
X-RAY DIFFRACTIONf_angle_d0.756110014
X-RAY DIFFRACTIONf_chiral_restr0.03781340
X-RAY DIFFRACTIONf_plane_restr0.0046268
X-RAY DIFFRACTIONf_dihedral_angle_d19.41043210
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 11.4834766904 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.130.4228300.3367551X-RAY DIFFRACTION11.33
3.13-3.590.31611000.27032135X-RAY DIFFRACTION43.78
3.59-4.520.30022350.27574446X-RAY DIFFRACTION90.61
4.52-57.150.21692400.19884929X-RAY DIFFRACTION99.08
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)
11.79335687119-0.757303848790.2018375411532.00017833993-0.3029373823550.680701961309-0.20503969894-0.618217429668-0.2210988125991.027411931670.1693697081740.464336181223-0.109841734486-0.247182099512-0.02100533742340.580450396190.3243004203470.08634181455210.352361774755-0.2050529047181.0071507467-12.97548060211.117487752221.6318131459
20.6441224891370.6911397186720.5834435691043.371490139372.022619292371.27835506001-0.294453760567-0.62666568699-0.1582791300390.878685067870.319288083722-0.2533527288041.197357925430.606141088683-0.08623591187770.8500236522810.398093869631-0.08849085804551.240635241630.03286890988120.496579214204-18.37780409951.432542355933.6669332105
32.31516394967-0.665343169136-0.04058939535682.665209929470.2963353390322.61925797929-0.165576871492-0.0986811561999-0.3718660321870.563878978611-0.168407045346-0.01620986452420.13925372360.1138456272220.1658621338390.222114042590.1611134523390.001753318440780.4394220985710.007533946479150.962420104439-6.999590850140.86214572665410.1631733643
41.90138701894-2.025247283330.6073474044032.7997939758-0.03527379871440.68782780619-0.0485066751851-0.267325402743-0.130757221540.9722516755960.5518258833340.596348222685-0.236088969578-0.554622134145-0.4493052364930.6956707611330.3967134680420.05944677417710.9349787666790.1789441197120.6998696441122.7219993907-8.8128130966920.5271228005
54.588430648112.632395683751.021673579425.55815999682-1.937316797081.788533540440.235493097679-0.8668332899630.4442579148831.42831732360.1095424941680.105001976416-1.03431518983-0.545792083006-0.3384720503571.006103580540.1331645139350.1208196442631.31559393930.1823987244410.91143860003518.5199106321-49.463435593634.6085053765
61.90307504821-0.3575963675820.8368064198371.453024445280.2802742988090.684746307763-0.244261101628-0.561049640199-0.3261266191340.6475348470710.305770717761-0.03168588920940.219720587191-0.213607214502-0.09546908335440.2730922380520.523524847650.245265111640.8569284058210.244145028510.79168046656819.16252967750.5149604305649.94803023397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 40 )AA1 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 92 )AA41 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 134 )AA93 - 134
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 40 )BB1 - 40
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 91 )BB41 - 91
6X-RAY DIFFRACTION6chain 'B' and (resid 92 through 134 )BB92 - 134

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