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- PDB-9e5t: env2 cobalamin riboswitch aptamer domain in complex with ethynyl-... -

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Basic information

Entry
Database: PDB / ID: 9e5t
Titleenv2 cobalamin riboswitch aptamer domain in complex with ethynyl-4-(4-phenyl-2,3,4-triazole)-guanidinium-cobalamin
ComponentsRNA (76-MER)
KeywordsRNA / riboswitch / aptamer / vitamin B12 / cobalamin
Function / homology: / : / N-methylpropane-1,3-diamine / RNA / RNA (> 10)
Function and homology information
Biological speciesmarine metagenome (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsOlenginski, L.T. / Zep, N.J. / Batey, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152029 United States
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Designing small molecules targeting a cryptic RNA binding site through base displacement.
Authors: Olenginski, L.T. / Wierzba, A.J. / Laursen, S.P. / Batey, R.T.
History
DepositionOct 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: 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 (76-MER)
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,59129
Polymers49,4632
Non-polymers4,12827
Water6,125340
1
A: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,78314
Polymers24,7321
Non-polymers2,05213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,80815
Polymers24,7321
Non-polymers2,07614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.206, 78.205, 77.101
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain RNA (76-MER)


Mass: 24731.697 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) marine metagenome (others)

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Non-polymers , 6 types, 367 molecules

#2: Chemical ChemComp-A1BE1 / ethynyl-4-(4-phenyl-2,3,4-triazole)-guanidinium-cobalamin / 3-[(3~{R},4~{S},5~{S},9~{S},10~{S},15~{S},19~{R},20~{R},21~{R})-4,9,20-tris(2-azanyl-2-oxidanylidene-ethyl)-5,15-bis(3-azanyl-3-oxidanylidene-propyl)-1-[2-[4-[1-(2-carbamimidamidoethyl)-1,2,3-triazol-4-yl]phenyl]ethynyl]-19-[3-[2-[[(2~{R},3~{S},4~{R},5~{S})-5-[5,6-di(methyl)benzimidazol-1-yl]-4-$l^{1}-oxidanyl-2-($l^{1}-oxidanylmethyl)oxolan-3-yl]oxy-$l^{1}-oxidanyl-phosphoryl]oxypropylamino]-3-oxidanylidene-propyl]-3,4,7,9,14,14,17,19-octamethyl-2-aza-22,23,24-triazonia-1$l^{5}-cobaltaoctacyclo[11.9.1.1^{1,8}.0^{2,6}.0^{3,21}.0^{16,23}.0^{18,22}.0^{11,24}]tetracosa-6,8(24),11,13(23),16,18(22)-hexaen-10-yl]propanamide


Mass: 1583.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C75H102CoN19O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-N3D / N-methylpropane-1,3-diamine


Mass: 88.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12N2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% (v/v) (+/-)-2-Methyl-2,4-pentanediol, 40 mM Sodium cacodylate trihydrate (pH 7.0), 12 mM Spermine tetrahydrochloride, 80 mM Potassium chloride, 20 mM Magnesium chloride hexahydrate. Hanging drop. 303.15 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.19→20 Å / Num. obs: 25509 / % possible obs: 98.7 % / Redundancy: 3.1 % / CC1/2: 0.99 / Rpim(I) all: 0.043 / Rrim(I) all: 0.078 / Χ2: 1.582 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.282.70.19123250.9440.9850.1380.2370.70991.1
2.28-2.372.80.18125170.9650.9910.130.2240.68297.7
2.37-2.4830.16825620.9710.9930.1160.2050.76499.5
2.48-2.613.20.15125450.9780.9940.1010.1830.87599.8
2.61-2.773.20.12425790.9840.9960.0830.151.05799.8
2.77-2.983.30.09825860.9910.9980.0640.1181.51199.8
2.98-3.283.30.07325980.9930.9980.0480.0882.117100
3.28-3.763.30.06225690.9930.9980.0420.0752.42899.7
3.76-4.723.20.05325990.9950.9990.0350.0642.58999.6
4.72-2030.0426290.9970.9990.0270.0482.52399.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→19.73 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2787 1991 7.89 %
Rwork0.2247 --
obs0.229 25227 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3280 269 340 3889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023940
X-RAY DIFFRACTIONf_angle_d0.5526142
X-RAY DIFFRACTIONf_dihedral_angle_d15.4591914
X-RAY DIFFRACTIONf_chiral_restr0.026766
X-RAY DIFFRACTIONf_plane_restr0.003160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.35431180.28621418X-RAY DIFFRACTION84
2.24-2.30.37291380.29471600X-RAY DIFFRACTION94
2.3-2.370.39351450.29281681X-RAY DIFFRACTION99
2.37-2.450.36971450.29581688X-RAY DIFFRACTION99
2.45-2.530.37951450.30431676X-RAY DIFFRACTION99
2.53-2.630.37861510.30731691X-RAY DIFFRACTION99
2.63-2.750.38881400.30891679X-RAY DIFFRACTION98
2.75-2.90.32581410.31181646X-RAY DIFFRACTION97
2.9-3.080.39311440.27361648X-RAY DIFFRACTION96
3.08-3.320.32291390.22131682X-RAY DIFFRACTION98
3.32-3.650.23181460.20731696X-RAY DIFFRACTION99
3.65-4.170.22391490.18721693X-RAY DIFFRACTION99
4.17-5.240.21731420.16681711X-RAY DIFFRACTION99
5.24-19.730.17971480.16161727X-RAY DIFFRACTION99

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