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- PDB-36le: RNA-dGMP complex with L-G-terminal primer -

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Basic information

Entry
Database: PDB / ID: 36le
TitleRNA-dGMP complex with L-G-terminal primer
ComponentsRNA (16-mer)
KeywordsRNA / Nonenzymatic RNA replication / Chirality
Function / homologyL-GUANOSINE-5'-MONOPHOSPHATE / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsEssex, J. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)2325198 United States
CitationJournal: To Be Published
Title: Effects of Chemically Activated L-Nucleotides on Nonenzymatic RNA Copying
Authors: Essex, J. / Jia, X. / Zhang, J. / Szostak, J.W.
History
DepositionJun 16, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 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: RNA (16-mer)
B: RNA (16-mer)
C: RNA (16-mer)
D: RNA (16-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,67019
Polymers18,3674
Non-polymers4,30415
Water81145
1
A: RNA (16-mer)
B: RNA (16-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2998
Polymers9,1832
Non-polymers2,1156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (16-mer)
D: RNA (16-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,37211
Polymers9,1832
Non-polymers2,1889
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.300, 47.423, 84.601
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: RNA chain
RNA (16-mer)


Mass: 4591.700 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-0G / L-GUANOSINE-5'-MONOPHOSPHATE


Type: L-RNA linking / Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O7P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 20% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.91165 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 20, 2025
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 1.73→42.3 Å / Num. obs: 14792 / % possible obs: 91.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 31.33 Å2 / CC1/2: 0.996 / Net I/σ(I): 6.4
Reflection shellResolution: 1.73→1.92 Å / Num. unique obs: 740 / CC1/2: 0.555 / % possible all: 49.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→42.3 Å / SU ML: 0.2535 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.8404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2586 1484 10.06 %
Rwork0.2237 13273 -
obs0.2273 14757 73.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.59 Å2
Refinement stepCycle: LAST / Resolution: 1.73→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1108 279 45 1432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081548
X-RAY DIFFRACTIONf_angle_d1.51272426
X-RAY DIFFRACTIONf_chiral_restr0.0551280
X-RAY DIFFRACTIONf_plane_restr0.005864
X-RAY DIFFRACTIONf_dihedral_angle_d22.0105752
LS refinement shellResolution: 1.73→1.79 Å
RfactorNum. reflection% reflection
Rfree0.1134 1 -
Rwork0.3275 740 -
obs--49.8 %
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)
13.15254514299-0.861248904082-0.07720070508823.401672887611.065204398793.008548964410.2276677816590.07363084237390.0855021266174-0.7788999751370.0963675429507-0.0328665260856-0.308605061706-0.177361888328-0.211016597780.397622180322-0.0370295560408-0.02292322839690.3170592432930.03406275636520.28202349922712.9912479507-2.76520605873-9.56417388992
22.130564157531.656348613420.5049548148661.911689073491.20848231491.29753217965-0.112295707813-0.1814355274990.112414480842-0.00755007202209-0.01208440755340.0603233744398-0.310130692661-0.08535533583720.08230704976410.303110760392-0.0125916910967-0.02643942107730.2494858173190.03566078254450.27306390013312.715336875-4.89304067763-2.68974985438
33.1457875560.5027861997991.513692187512.049964811650.0330565884382.804098763220.203988465988-0.245828481231-0.1691061178740.3156164226410.0394845746078-0.157516376374-0.05730087405040.0781233827612-0.2301082145750.2925901272580.0193886795136-0.007293136567140.278569388372-0.05931219603670.2585321820578.8086266609920.5964087467-19.6351783153
43.56393733645-0.426391955131.156179272452.10077863664-0.7034346480153.237969777180.6067669623530.366239354239-0.287788104759-0.251042979152-0.1664240412280.1058567313940.529429376092-0.0595103774275-0.3778626495280.314885981936-4.7129471291E-5-0.03183855853480.22729873099-0.06027698323920.2677379750519.63127886318.4330371139-26.7909344043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 13 )AA5 - 13
2X-RAY DIFFRACTION2chain 'B' and (resid 5 through 13 )BE5 - 13
3X-RAY DIFFRACTION3chain 'C' and (resid 5 through 13 )CI5 - 13
4X-RAY DIFFRACTION4chain 'D' and (resid 5 through 13 )DM5 - 13

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