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- PDB-9hrg: Crystal structure of the Class V (G61A) GTP aptamer variant in co... -

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Basic information

Entry
Database: PDB / ID: 9hrg
TitleCrystal structure of the Class V (G61A) GTP aptamer variant in complex with GTP
ComponentsClass V (G61A) GTP aptamer
KeywordsRNA / RNA-aptamer GTP G-quadruplex
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 (G61A) GTP aptamer
B: Class V (G61A) GTP aptamer
C: Class V (G61A) GTP aptamer
D: Class V (G61A) GTP aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,84528
Polymers88,1484
Non-polymers2,69724
Water5,044280
1
A: Class V (G61A) GTP aptamer
B: Class V (G61A) GTP aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,42314
Polymers44,0742
Non-polymers1,34912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Class V (G61A) GTP aptamer
D: Class V (G61A) GTP aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,42314
Polymers44,0742
Non-polymers1,34912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.215, 126.247, 68.601
Angle α, β, γ (deg.)90.000, 90.500, 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_1(chain "A" and (resid 1 through 29 or resid 31...
d_2ens_1(chain "B" and (resid 1 through 29 or resid 31...
d_3ens_1(chain "C" and (resid 1 through 29 or resid 31...
d_4ens_1(chain "D" and (resid 1 through 29 or resid 31...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GGCCAA1 - 41 - 4
d_12KKKKAE101
d_21GGCCBB1 - 41 - 4
d_22KKKKBK101
d_31GGCCCC1 - 41 - 4
d_32KKKKCQ101
d_41GGCCDD1 - 41 - 4
d_42KKKKDW101

NCS oper:
IDCodeMatrixVector
1given(-0.999950436452, -0.00971552718699, 0.00217558498443), (-0.00962765065589, 0.999257838349, 0.0372971961587), (-0.00253633227196, 0.0372744018051, -0.999301849287)-30.6697016684, 0.563035159789, -36.6070076733
2given(-0.999997446977, -0.00185004981407, -0.00129744170064), (0.00182320283492, -0.99979030092, 0.0203968163423), (-0.00133490475459, 0.0203943987693, 0.999791121449)-2.12793060468, 48.1955330968, -0.282872545218
3given(0.999991608552, 0.0033120991586, 0.00241097998443), (0.00345624022962, -0.998041226229, -0.062464110896), (0.00219937009094, 0.0624719196576, -0.998044298629)-23.3024730202, 46.8367987099, -37.0798471588

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Components

#1: RNA chain
Class V (G61A) GTP aptamer


Mass: 22036.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 65.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
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: Jun 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.05→34.6 Å / Num. obs: 54475 / % possible obs: 97.82 % / Redundancy: 7.1 % / Biso Wilson estimate: 58.29 Å2 / Rmerge(I) obs: 0.0634 / Rpim(I) all: 0.0261 / Net I/σ(I): 13.23
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 5416 / Rpim(I) all: 0.877 / % possible all: 97.85

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
PHENIX1.20.1_4487refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
pointlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→34.6 Å / SU ML: 0.3327 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.1346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2325 2715 4.99 %
Rwork0.2068 51709 -
obs0.2081 54424 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.68 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5840 148 280 6268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00566764
X-RAY DIFFRACTIONf_angle_d1.154710564
X-RAY DIFFRACTIONf_chiral_restr0.05311396
X-RAY DIFFRACTIONf_plane_restr0.0067280
X-RAY DIFFRACTIONf_dihedral_angle_d16.91663368
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.735901191644
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.334866348362
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.780336248304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.40961460.40532738X-RAY DIFFRACTION97.33
2.09-2.130.38981160.37742702X-RAY DIFFRACTION98.43
2.13-2.170.36541480.34882731X-RAY DIFFRACTION98.03
2.17-2.220.38331580.33562637X-RAY DIFFRACTION95.29
2.22-2.270.35281640.31652628X-RAY DIFFRACTION96.01
2.27-2.330.33771520.2882704X-RAY DIFFRACTION98.58
2.33-2.390.3041490.26162767X-RAY DIFFRACTION98.55
2.39-2.460.26681530.24362705X-RAY DIFFRACTION98.45
2.46-2.540.33081460.25722730X-RAY DIFFRACTION98.29
2.54-2.630.3371450.26962738X-RAY DIFFRACTION98.63
2.63-2.730.33811280.2862743X-RAY DIFFRACTION98.29
2.73-2.860.35521260.3162745X-RAY DIFFRACTION98.49
2.86-3.010.29041290.30262750X-RAY DIFFRACTION99
3.01-3.20.31360.23052659X-RAY DIFFRACTION95.33
3.2-3.450.26341660.22392677X-RAY DIFFRACTION96.57
3.45-3.790.24381380.19222784X-RAY DIFFRACTION99.49
3.79-4.340.1711460.15562776X-RAY DIFFRACTION99.15
4.34-5.460.1441300.14912789X-RAY DIFFRACTION99.35
5.46-34.60.17761390.16862706X-RAY DIFFRACTION95.53
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)
11.210813856620.136763603207-0.05009683416021.07324392739-0.08973868115171.15784400685-0.00540781635629-0.2942777271770.163131643728-0.02615990818110.028144537844-0.1565565121410.233130511490.3038582445652.97942781378E-50.616356418726-0.0004726474466920.0006893283301860.599797568325-0.07144509558210.58436332936-5.1994978303441.1822463216-13.830584077
21.53760765246-0.3100863914520.4190272813091.32574375269-0.4147495227361.19488082159-0.0596257392278-0.0930315333670.180841875187-0.0121552983460.1510829630710.2420674109810.0818246479702-0.266052510082-0.0002985811457650.560041454407-0.05847817169260.01808145329610.489780544207-0.02486365482230.537871385549-25.859034943841.2405811121-21.2099211385
31.222196528180.583689534719-0.1174572077791.065099576210.287147895131.27471970311-0.0621281073851-0.240590239062-0.1264355664370.0742456155407-0.01528177512670.131341351188-0.153302611372-0.282662822202-0.000207664591180.6149894634030.05708315148670.01136026600590.5880512752940.03812846968470.5817649650023.022394624916.73209819125-13.2597265921
41.61090314205-0.195750642048-0.1942416323741.426390606040.6906508657791.34526399453-0.0426635445360.111669568883-0.2439353432880.03018048510920.194985546575-0.232969571568-0.01554727924560.384372577213-0.0001457640783880.5300430784480.00675596056296-0.02630843998660.48153182471-0.009657487767830.540789094757-28.41492002946.58016557435-20.6716706451
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:102)AA - D1 - 102
2X-RAY DIFFRACTION2(chain B and resseq 1:102)BE - H1 - 102
3X-RAY DIFFRACTION3(chain C and resseq 1:102)CI - L1 - 102
4X-RAY DIFFRACTION4(chain D and resseq 1:102)DM - P1 - 102

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