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- PDB-9hrf: Crystal structure of the Class V (UU) GTP aptamer variant in comp... -

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Basic information

Entry
Database: PDB / ID: 9hrf
TitleCrystal structure of the Class V (UU) GTP aptamer variant in complex with GTP
ComponentsClass V (UU) GTP aptamer
KeywordsRNA / RNA-aptamer GTP G-quadruplex potassium ion
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsStafflinger, H. / Woehnert, J. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WO 901/1-1 Germany
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Crystal structure of the class V GTP-binding RNA aptamer bound to its ligand: GTP recognition by a topologically complex intermolecular G-quadruplex.
Authors: Stafflinger, H. / Neissner, K. / Bartsch, S. / Pichler, A.K. / Bartosik, K. / Dhamotharan, K. / Abele, R. / Duchardt-Ferner, E. / Micura, R. / Schindelin, H. / Wohnert, J.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class V (UU) GTP aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3638
Polymers22,6651
Non-polymers6977
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-38 kcal/mol
Surface area12580 Å2
Unit cell
Length a, b, c (Å)89.351, 89.351, 56.395
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain Class V (UU) GTP aptamer


Mass: 22665.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: methylpentanediol, sodium chloride, potassium chloride, magnesium chloride, spermine, cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→19.98 Å / Num. obs: 30618 / % possible obs: 76.09 % / Redundancy: 26.2 % / Rmerge(I) obs: 0.0722 / Rpim(I) all: 0.0145 / Net I/σ(I): 20.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 24.8 % / Mean I/σ(I) obs: 0.37 / Num. unique obs: 311 / Rpim(I) all: 1.37 / % possible all: 10.37

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
pointlessdata scaling
PHASERphasing
Cootmodel building
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.98 Å / SU ML: 0.1731 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2173 1160 4.97 %
Rwork0.1806 22162 -
obs0.1824 23322 76.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.19 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1501 38 164 1703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01741733
X-RAY DIFFRACTIONf_angle_d1.99432706
X-RAY DIFFRACTIONf_chiral_restr0.0918359
X-RAY DIFFRACTIONf_plane_restr0.017872
X-RAY DIFFRACTIONf_dihedral_angle_d17.9128866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.670.3662210.2894416X-RAY DIFFRACTION11.65
1.67-1.760.3725640.27861076X-RAY DIFFRACTION30.37
1.76-1.870.3121100.2532310X-RAY DIFFRACTION64.21
1.87-2.020.27651870.23543591X-RAY DIFFRACTION99.68
2.02-2.220.25571890.22683596X-RAY DIFFRACTION99.97
2.22-2.540.25312010.22173631X-RAY DIFFRACTION100
2.54-3.20.26391980.19363687X-RAY DIFFRACTION99.97
3.2-19.980.15951900.14233855X-RAY DIFFRACTION99.93
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)
10.938696637520.601313301722-1.63990694371.32516570328-1.545625790832.872430628370.1571887237170.421538722690.506291736176-0.188062460250.15924951490.368329052806-0.134656243362-0.19438577333-0.2242913112980.3116862760510.02088622597420.08011761251810.2977130919770.01890357127960.4119556914659.5164328801127.8609906684-25.5348876722
22.033038964761.384863024010.6766320151860.450717167417-0.2060028526831.66897100246-0.0547863408226-0.2188846219180.1144567809510.1752843748090.0358047336940.202683683851-0.0737351862391-0.494463232779-0.008311616372180.211488392750.01053777087240.05394703902260.251781716981-0.01038936512220.21323092312-12.137415344732.9216453299-6.8860165807
33.07700369637-1.1370971559-0.735874881025.93067608652.800668273363.128205938420.319439549146-0.1687607650880.06967716963760.343418152301-0.244181163039-0.01054878906-0.102750737569-0.223769542875-0.09021538421640.334759234904-0.09853475888990.04893370989060.287381685840.03818133667240.236029747495-12.711199826323.2288939271-4.09036976779
41.197154377890.3104577080750.6696532261740.8234124627930.5384463761662.19679893721-0.1026839908570.0942397219437-0.0905943704164-0.1434771021110.0195772403137-0.2106461672780.2920608269170.5290680405230.1187680282470.2619999910890.08884694229260.07245893481350.2327241069670.04362306581160.1979450823687.7711272476229.705410848-20.2940732349
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 30 )AA11 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 50 )AA31 - 50
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 70 )AA51 - 70

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