PDB-9hrd: Crystal structure of the Class V GTP aptamer in complex with GTP

ID or keywords:

Entry

Database: PDB / ID: 9hrd

Title

Crystal structure of the Class V GTP aptamer in complex with GTP

Components

Class V GTP aptamer

Keywords

RNA / RNA-aptamer GTP G-quadruplex potassium ion

Function / homology

GUANOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10)

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

Stafflinger, H. / Woehnert, J. / Schindelin, H.

Funding support

Germany, 1items

Citation

Journal: 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

Deposition	Dec 18, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 14, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9hrd.cif.gz	594.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9hrd.ent.gz	380.8 KB	Display	PDB format
PDBx/mmJSON format	9hrd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hr/9hrd ftp://data.pdbj.org/pub/pdb/validation_reports/hr/9hrd	HTTPS FTP

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Related structure data

Related structure data	9hrfC 9hrgC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: Class V GTP aptamer

B: Class V GTP aptamer

C: Class V GTP aptamer

D: Class V GTP aptamer

hetero molecules

93.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Class V GTP aptamer

hetero molecules

B: Class V GTP aptamer

hetero molecules

defined by author
Evidence: SAXS
46.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Class V GTP aptamer

D: Class V GTP aptamer

hetero molecules

defined by author
46.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	52.268, 127.216, 68.368
Angle α, β, γ (deg.)	90.000, 90.455, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: C / End label comp-ID: C / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 2 - 68 / Label seq-ID: 2 - 68

Dom-ID	Component-ID	Ens-ID
1	1	1
2	1	1
3	2	2
4	2	2
5	3	3
6	3	3
7	4	4
8	4	4
9	5	5
10	5	5
11	6	6
12	6	6

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: RNA chain	Class V GTP aptamer Mass: 22052.996 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-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 8 / 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.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.75 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: methylpentanediol, potasium chloride, manganese chloride, spermine, cacodylate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.892 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.892 Å / Relative weight: 1
Reflection	Resolution: 2.5→20.001 Å / Num. obs: 30103 / % possible obs: 97.32 % / Redundancy: 6.8 % / R_merge(I) obs: 0.0897 / R_pim(I) all: 0.0374 / Net I/σ(I): 11.23
Reflection shell	Resolution: 2.5→2.59 Å / Mean I/σ(I) obs: 0.75 / Num. unique obs: 2966 / R_pim(I) all: 0.877

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
PHENIX	1.20.1-4487	refinement
Coot		model building
PHASER		phasing
Aimless		data scaling
pointless		data scaling
XDS		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 2.5→20.001 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.953 / SU B: 33.61 / SU ML: 0.304 / Cross valid method: FREE R-VALUE / ESU R: 0.639 / ESU R Free: 0.283
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2378	1530	5.083 %
R_work	0.2003	28570	-
all	0.202	-	-
obs	-	30100	97.317 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 79.848 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.544 Å²	0 Å²	0.297 Å²
2-	-	-1.656 Å²	-0 Å²
3-	-	-	1.108 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→20.001 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	5752	276	74	6102

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.011	6752
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.019	2716
X-RAY DIFFRACTION	r_angle_refined_deg	1.873	1.857	10554
X-RAY DIFFRACTION	r_angle_other_deg	0.531	1.683	6608
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.401	5	210
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	1408
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	3390
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1044
X-RAY DIFFRACTION	r_nbd_refined	0.396	0.2	1312
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.21	0.2	3001
X-RAY DIFFRACTION	r_nbtor_refined	0.245	0.2	2385
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	1828
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.243	0.2	177
X-RAY DIFFRACTION	r_metal_ion_refined	0.019	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.139	0.2	46
X-RAY DIFFRACTION	r_nbd_other	0.23	0.2	20
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.302	0.2	4
X-RAY DIFFRACTION	r_scbond_it	5.718	5.508	6752
X-RAY DIFFRACTION	r_scbond_other	5.718	5.508	6752
X-RAY DIFFRACTION	r_scangle_it	8.348	10.013	10554
X-RAY DIFFRACTION	r_scangle_other	8.348	10.013	10555
X-RAY DIFFRACTION	r_lrange_it	10.524	70.671	9603
X-RAY DIFFRACTION	r_lrange_other	10.518	70.69	9592
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.045	0.05	7108
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.037	0.05	7167
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.042	0.05	7150
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.038	0.05	7148
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.038	0.05	7193
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.049	0.05	7156

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.04521	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.04521	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.03656	0.05011
2	4	A	X-RAY DIFFRACTION	Local ncs	0.03656	0.05011
3	5	A	X-RAY DIFFRACTION	Local ncs	0.04168	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.04168	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.03814	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.03814	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.03844	0.05011
5	10	A	X-RAY DIFFRACTION	Local ncs	0.03844	0.05011
6	11	A	X-RAY DIFFRACTION	Local ncs	0.04885	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.04885	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.5-2.564	0.453	98	0.443	2059	0.444	2244	0.828	0.804	96.123	0.442
2.564-2.633	0.411	133	0.411	1979	0.411	2205	0.857	0.865	95.7823	0.403
2.633-2.708	0.353	105	0.382	1964	0.38	2129	0.9	0.906	97.1818	0.375
2.708-2.79	0.457	95	0.385	1885	0.388	2072	0.859	0.924	95.5598	0.379
2.79-2.88	0.376	122	0.344	1832	0.346	2019	0.911	0.943	96.7806	0.333
2.88-2.978	0.415	97	0.298	1778	0.304	1935	0.912	0.954	96.8992	0.274
2.978-3.088	0.295	106	0.259	1722	0.261	1878	0.952	0.969	97.3376	0.236
3.088-3.211	0.272	70	0.204	1689	0.206	1794	0.961	0.983	98.049	0.193
3.211-3.35	0.255	95	0.208	1613	0.211	1745	0.975	0.983	97.8797	0.203
3.35-3.509	0.239	84	0.204	1540	0.206	1657	0.962	0.98	98.0084	0.199
3.509-3.692	0.227	68	0.184	1455	0.186	1576	0.973	0.984	96.6371	0.179
3.692-3.908	0.185	71	0.177	1387	0.178	1509	0.981	0.985	96.6203	0.177
3.908-4.166	0.206	74	0.17	1329	0.172	1413	0.974	0.986	99.2923	0.172
4.166-4.484	0.226	59	0.172	1255	0.174	1321	0.973	0.984	99.4701	0.176
4.484-4.887	0.2	58	0.157	1171	0.159	1236	0.975	0.985	99.4337	0.164
4.887-5.424	0.175	48	0.16	1065	0.161	1114	0.979	0.985	99.9102	0.172
5.424-6.187	0.184	52	0.167	942	0.168	997	0.979	0.985	99.6991	0.179
6.187-7.403	0.249	36	0.17	809	0.172	862	0.979	0.986	98.0278	0.188
7.403-9.818	0.19	45	0.165	645	0.167	690	0.979	0.986	100	0.181
9.818-20.001	0.112	14	0.132	451	0.131	465	0.994	0.991	100	0.158

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.542	0.7709	-0.9964	2.2099	-0.0918	2.8589	-0.3212	-0.197	0.0527	-0.0282	0.1823	-0.2015	0.6949	0.1848	0.1389	0.187	0.0425	-0.0012	0.2201	-0.0122	0.0933	-4.6256	40.7979	-13.4985
2	3.0026	-0.8125	-0.4347	3.0144	0.3896	3.0382	-0.3286	-0.0709	0.2506	-0.0723	0.211	0.2434	0.4821	-0.2073	0.1176	0.1213	-0.0584	-0.0183	0.121	-0.0135	0.0675	-25.5288	40.8915	-21.0867
3	3.0071	1.0112	1.3741	2.2613	0.6827	3.2705	-0.2065	-0.0977	-0.0952	0.0824	0.1056	0.186	-0.5643	-0.2039	0.1008	0.1287	0.0517	0.0304	0.1796	0.0092	0.1034	3.2147	7.0615	-13.1612
4	2.6805	-0.0302	0.4537	2.6906	0.4994	2.809	-0.234	0.089	-0.2625	0.0566	0.2184	-0.324	-0.4426	0.2994	0.0156	0.0878	-0.0289	-0.0019	0.1424	-0.0174	0.0715	-28.0765	6.9255	-20.79

Refinement TLS group

Selection: ALL

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