PDB-9yd4: RNA primer non-enzymatic extension product with DNA substrate

Keywords

RNA / Nonenzymatic RNA primer extension / Product / RNA duplex / Origin of Life

Function / homology

: / DNA/RNA hybrid / DNA/RNA hybrid (> 10)

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.658 Å

Authors

Fang, Z. / Szostak, J.W.

Funding support

United States, 2items

Citation

Journal: To Be Published
Title: Nonenzymatic RNA copying with deoxypurine
Authors: Fang, Z. / Szostak, J.W.

History

Deposition	Sep 21, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9yd4.cif.gz	38.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9yd4.ent.gz		Display	PDB format
PDBx/mmJSON format	9yd4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9yd4_validation.pdf.gz	1018 KB	Display	wwPDB validaton report
Full document	9yd4_full_validation.pdf.gz	1 MB	Display
Data in XML	9yd4_validation.xml.gz	7.9 KB	Display
Data in CIF	9yd4_validation.cif.gz	10.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yd/9yd4 ftp://data.pdbj.org/pub/pdb/validation_reports/yd/9yd4	HTTPS FTP

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Related structure data

Related structure data	9yd3C 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	#130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: DNA/RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-D(P*G)-3')

B: DNA/RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-D(P*G)-3')

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	48.254, 48.254, 82.532
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	150
Space group name H-M	P321

Components on special symmetry positions

ID	Model	Components
1	1	A-205- HOH
2	1	A-248- HOH
3	1	B-250- HOH
4	1	B-257- HOH
5	1	B-258- HOH

#1: DNA/RNA hybrid	DNA/RNA (5'-R((LCC)P(LCC)P(LCC)P(LCG)PAPCPUPUPAPAPGPUPCPG)-D(PG)-3') Mass: 4762.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source*: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-A1CWA / (2-azanylimidazol-1-yl)-[[(2~{R},3~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy]phosphinic acid / 5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy)phosphoryl]-2'-deoxyguanosine Type: DNA linking / Mass: 412.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₃H₁₇N₈O₆P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.9 Å³/Da / Density % sol: 57.62 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.05 M HEPES pH 7.0, 0.2 M Ammonium acetate, 0.15 M Magnesium acetate, 10% w/v Polyethylene glycol 6,000.

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Data collection

Diffraction	Mean temperature: 99 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033175 Å
Detector	Type: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Jun 23, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033175 Å / Relative weight: 1
Reflection	Resolution: 1.658→50 Å / Num. obs: 13714 / % possible obs: 99.6 % / Redundancy: 8.7 % / CC_1/2: 0.963 / CC star: 0.991 / R_merge(I) obs: 0.115 / R_pim(I) all: 0.044 / R_rim(I) all: 0.124 / Χ²: 0.903 / Net I/σ(I): 22.3
Reflection shell	Resolution: 1.658→1.69 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.287 / Mean I/σ(I) obs: 8 / Num. unique obs: 646 / CC_1/2: 0.992 / CC star: 0.998 / R_pim(I) all: 0.116 / R_rim(I) all: 0.311 / Χ²: 0.964 / % possible all: 96.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.658→37.282 Å / Cor.coef. F_o:F_c: 0.896 / Cor.coef. F_o:F_c free: 0.87 / SU B: 2.444 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.141
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2891	559	4.826 %
R_work	0.2568	11024	-
all	0.258	-	-
obs	-	11583	84.105 %

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: 18.391 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.003 Å²	0.001 Å²	0 Å²
2-	-	0.003 Å²	-0 Å²
3-	-	-	-0.009 Å²

Refinement step

Cycle: LAST / Resolution: 1.658→37.282 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	642	63	122	827

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.016	784
X-RAY DIFFRACTION	r_bond_other_d	0.027	0.023	354
X-RAY DIFFRACTION	r_angle_refined_deg	2.575	2.23	1200
X-RAY DIFFRACTION	r_angle_other_deg	3.714	2.357	832
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.055	5	16
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	152
X-RAY DIFFRACTION	r_chiral_restr_other	1.95	0.2	20
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.021	418
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.023	136
X-RAY DIFFRACTION	r_nbd_refined	0.128	0.2	63
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.199	0.2	424
X-RAY DIFFRACTION	r_nbtor_refined	0.251	0.2	313
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.236	0.2	204
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.211	0.2	80
X-RAY DIFFRACTION	r_metal_ion_refined	0.07	0.2	11
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.141	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.15	0.2	38
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.245	0.2	21
X-RAY DIFFRACTION	r_scbond_it	2.791	2.223	784
X-RAY DIFFRACTION	r_scbond_other	2.79	2.228	785
X-RAY DIFFRACTION	r_scangle_it	4.351	4.06	1200
X-RAY DIFFRACTION	r_scangle_other	4.35	4.065	1201
X-RAY DIFFRACTION	r_lrange_it	6.366	25.521	1133
X-RAY DIFFRACTION	r_lrange_other	6.254	25.368	1089

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
1.658-1.701	0.359	30	0.239	389	0.246	997	0.883	0.967	42.0261	0.2
1.701-1.747	0.373	28	0.22	429	0.229	974	0.938	0.972	46.9199	0.187
1.747-1.798	0.242	43	0.283	457	0.279	936	0.963	0.952	53.4188	0.256
1.798-1.853	0.312	24	0.255	541	0.258	927	0.938	0.955	60.9493	0.219
1.853-1.913	0.265	26	0.269	615	0.269	899	0.95	0.951	71.3014	0.266
1.913-1.98	0.379	43	0.298	795	0.302	847	0.88	0.939	98.9374	0.29
1.98-2.055	0.266	35	0.278	797	0.277	832	0.961	0.949	100	0.258
2.055-2.139	0.323	46	0.241	756	0.244	802	0.937	0.965	100	0.228
2.139-2.233	0.297	43	0.255	731	0.258	774	0.941	0.958	100	0.252
2.233-2.342	0.242	28	0.246	715	0.246	743	0.957	0.96	100	0.261
2.342-2.468	0.331	38	0.226	672	0.232	712	0.929	0.967	99.7191	0.25
2.468-2.617	0.201	21	0.223	647	0.223	673	0.979	0.969	99.2571	0.262
2.617-2.797	0.214	27	0.231	614	0.23	643	0.961	0.968	99.689	0.296
2.797-3.02	0.241	22	0.245	571	0.245	596	0.97	0.965	99.4966	0.311
3.02-3.306	0.297	29	0.266	512	0.268	548	0.971	0.94	98.7226	0.428
3.306-3.692	0.274	14	0.235	489	0.236	505	0.97	0.965	99.604	0.34
3.692-4.256	0.286	17	0.242	437	0.243	454	0.932	0.95	100	0.314
4.256-5.196	0.292	18	0.232	365	0.235	388	0.978	0.963	98.7113	0.441
5.196-7.278	0.234	15	0.29	299	0.287	314	0.981	0.953	100	0.397
7.278-37.282	0.59	12	0.613	192	0.612	204	0.835	0.868	100	0.697

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