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- PDB-8tsv: Crystal structure of the Zika virus stem-loop A (SLA) top stem -

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Basic information

Entry
Database: PDB / ID: 8tsv
TitleCrystal structure of the Zika virus stem-loop A (SLA) top stem
ComponentsZika virus stem-loop A (SLA) top stem
KeywordsRNA / Zika virus / Flavivirus / RNA structure / stem-loop A
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesZika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsTipo, J. / Gottipati, K. / Choi, K.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI 187856 United States
CitationJournal: Rna / Year: 2024
Title: High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules.
Authors: Tipo, J. / Gottipati, K. / Choi, K.H.
History
DepositionAug 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zika virus stem-loop A (SLA) top stem
B: Zika virus stem-loop A (SLA) top stem
C: Zika virus stem-loop A (SLA) top stem
D: Zika virus stem-loop A (SLA) top stem
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4647
Polymers32,1834
Non-polymers2803
Water7,927440
1
A: Zika virus stem-loop A (SLA) top stem
B: Zika virus stem-loop A (SLA) top stem
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1883
Polymers16,0922
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-23 kcal/mol
Surface area9000 Å2
MethodPISA
2
C: Zika virus stem-loop A (SLA) top stem
D: Zika virus stem-loop A (SLA) top stem
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2764
Polymers16,0922
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-11 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.226, 52.532, 53.670
Angle α, β, γ (deg.)63.600, 88.080, 85.940
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: RNA chain
Zika virus stem-loop A (SLA) top stem


Mass: 8045.820 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: A GGGCCC linker sequence is used to connect the antiparallel strands of the top stem
Source: (synth.) Zika virus
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: Sodium Acetate, Magnesium Sulfate, Lithium Sulfate, Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→29.15 Å / Num. obs: 43189 / % possible obs: 96.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 13.52 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.02 / Rrim(I) all: 0.04 / Net I/σ(I): 39
Reflection shellResolution: 1.51→1.54 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.144 / Num. unique obs: 2043 / CC1/2: 0.971 / CC star: 0.993 / Rpim(I) all: 0.096 / Rrim(I) all: 0.174 / Χ2: 0.816 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata collection
HKL-2000data scaling
PHENIXphasing
PHENIXmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→29.15 Å / SU ML: 0.1294 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 17.5025
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.175 1992 4.62 %
Rwork0.1554 41156 -
obs0.1563 43148 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.76 Å2
Refinement stepCycle: LAST / Resolution: 1.51→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2107 17 440 2564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092365
X-RAY DIFFRACTIONf_angle_d1.35083676
X-RAY DIFFRACTIONf_chiral_restr0.0578495
X-RAY DIFFRACTIONf_plane_restr0.014998
X-RAY DIFFRACTIONf_dihedral_angle_d10.21481186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.550.20711340.17252807X-RAY DIFFRACTION90.91
1.55-1.590.20971410.15132880X-RAY DIFFRACTION95.06
1.59-1.640.15671340.14312917X-RAY DIFFRACTION95.2
1.64-1.690.17141460.14082888X-RAY DIFFRACTION95.23
1.69-1.750.17061420.142909X-RAY DIFFRACTION96
1.75-1.820.171530.14682974X-RAY DIFFRACTION96.01
1.82-1.90.18351310.15422903X-RAY DIFFRACTION96.53
1.9-20.2051540.16122990X-RAY DIFFRACTION96.95
2-2.130.20341430.16782925X-RAY DIFFRACTION97.06
2.13-2.290.19161480.18242992X-RAY DIFFRACTION97.58
2.29-2.520.20261370.18172985X-RAY DIFFRACTION97.81
2.52-2.890.22171410.18332999X-RAY DIFFRACTION98.16
2.89-3.640.16141500.15423009X-RAY DIFFRACTION98.29
3.64-29.150.12771380.12472978X-RAY DIFFRACTION97.74
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)
10.600729572997-0.3337333956130.4445969983230.8853726167370.1423272157920.4854487822810.0776192881828-0.101938737722-0.06684964393560.0483243728145-0.0554576326910.1559829233220.101964292749-0.0498610165957-0.02092601220630.120844917965-0.002228575505250.007997114529920.126855254360.004106989670810.1194964456784.96361548531-13.08589284174.63376639878
23.69989527167-0.857537972997-0.7283574986570.4555495126820.3161094487840.951515186525-0.204210317521-0.5962029457120.02912247914980.1426073155770.08741394374990.2124951267470.252249484357-0.23790858050.09800867977160.189065558019-0.01370796980120.01219346410420.295948219594-0.02144345774640.1639423776031.92744712155-20.715052437620.5426741677
33.035559372890.06241430375530.8297380880553.52882659524-1.043702194212.718043517560.121741524771-0.7119502811470.03714913103680.3926319656360.09032495781370.423051553160.20062495729-0.015572372342-0.2063831757510.2024215628160.0172269932780.04091517793360.305263164636-0.004312155129690.186105711868-15.7800243222-25.652230955324.9794502498
40.751892972571-0.81424065759-0.928313473822.005729352120.6244714436033.485797817470.1364196243340.0987053490169-0.0808320201904-0.274493796150.08330036614080.08019286874840.400578763414-0.104919486927-0.2253907010840.1762894183360.00211882211437-0.03093819081340.109514165194-0.01669507953350.0981183754958-9.24863894175-35.668428243439.0690703412
50.5194903216440.1799770248021.099076716130.2927871527040.3588664269612.245703410930.1516512964460.280521453225-0.0130521404126-0.315360408550.0779073459628-0.04411506981360.0295902701240.403894873343-0.1996679287790.1877582112120.02506795390930.01027425733580.179641520018-0.01460815845690.112668187337-8.47529012899-29.643463063130.8854063583
63.608587688051.379756700050.8529869045850.9833613222140.4090670341180.419884476491-0.1479833937940.1487745787420.270915130384-0.2884817141210.13705371469-0.169288583727-0.0172698718040.2007048645890.01277911699150.17212309675-0.01760497794680.01086977748770.2205275132130.003197625795810.212830082546-8.17656142579-17.948592692415.0729937668
70.6394142104230.0814075374560.1916171149121.49689799636-0.04071326093350.09533379383550.05203729248020.005118043424380.0836183220368-0.0662840669928-0.084380026002-0.00440933090945-0.02462932435890.02623560437130.03833170735190.1196560668690.000625562446898-0.0009727260778840.116969328485-0.009327173303540.1333134589597.32831065535-11.80709477842.25765881012
81.01905966835-0.1799456242670.5244004609611.21022821839-0.2109316814530.253846800017-0.1579375583280.2357531564750.144947311195-0.2029066946450.0952651013366-0.09554596298350.01532343957390.08919221225120.06259501307510.135872329184-0.03419668562040.01211227362640.1235381494480.008490143331630.1208561179785.25835659169-7.6701315139538.7856578157
90.813672970317-0.866581430698-0.625909793951.260337821761.14977521793.340662836510.0455238231728-0.318783327230.176754210320.1990634355490.247252027644-0.0916342610082-0.1793968789770.000367741099812-0.2876168810770.1722253612180.02075276580950.01116088828880.200288981601-0.0151880928940.14233605109722.46183061925.9391035089413.6440031209
102.573312846120.2742676007240.2103391456492.48940379567-0.1764314253092.519640297520.0132780154109-0.3297722385620.02605610870580.2198399726380.1656170473630.0745893275724-0.141057063343-0.0742272694653-0.1622462431620.1146332409640.01203457561980.01232297800920.128766651876-0.01586411451930.1009059705419.86515943261.659137341887.24866035366
111.102244947110.695512224882-0.1174925132083.072229122974.366693980477.5964847502-0.258093389311-0.08221763481740.07290837583541.103138441680.41384625914-0.4152037077681.132081077341.00030014219-0.1622116258810.5806951541140.1817747797230.01094655065780.4159749011460.006985684867950.26237816661123.5289160822.8824414379124.2996125869
122.3458592977-0.473510840721-1.560702894953.28800569964-1.656390467522.25700929560.23789426516-0.8176862731220.2797050653040.1036764337110.4991193204890.6729177572690.111783051194-0.605765657118-0.7289526866830.415863333604-0.108339035558-0.0114840139820.5993534573220.1135852472990.4481010734047.671346395621.8699216618629.3942297544
133.186006674750.685837588499-0.1162809838320.683577289448-0.02898001200280.141547074418-0.09893343590850.0140184229914-0.185732612314-0.04238662637220.04428298631950.0221260800130.06738771838730.01954113423910.04145377135240.115940931104-0.00273302203128-0.00716294648710.09466165532450.001883858341410.1419122776220.257315244991-11.878056077145.538487799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )AA1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 15 )AA11 - 15
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 20 )AA16 - 20
4X-RAY DIFFRACTION4chain 'A' and (resid 21 through 25 )AA21 - 25
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 10 )BB1 - 10
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 15 )BB11 - 15
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 25 )BB16 - 25
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 15 )CC1 - 15
9X-RAY DIFFRACTION9chain 'C' and (resid 16 through 25 )CC16 - 25
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 5 )DD1 - 5
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 10 )DD6 - 10
12X-RAY DIFFRACTION12chain 'D' and (resid 11 through 15 )DD11 - 15
13X-RAY DIFFRACTION13chain 'D' and (resid 16 through 25 )DD16 - 25

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