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- PDB-9e5o: env2 cobalamin riboswitch aptamer domain in complex with ethynyl-... -

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Basic information

Entry
Database: PDB / ID: 9e5o
Titleenv2 cobalamin riboswitch aptamer domain in complex with ethynyl-pyrene-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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsOlenginski, L.T. / 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)53,53529
Polymers49,4632
Non-polymers4,07227
Water10,160564
1
A: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,75514
Polymers24,7321
Non-polymers2,02413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,78015
Polymers24,7321
Non-polymers2,04814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.195, 77.898, 80.263
Angle α, β, γ (deg.)90.00, 90.01, 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, 591 molecules

#2: Chemical ChemComp-A1BEW / ethynyl-pyrene-cobalamin / [(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] 1-[3-[(3~{R},4~{R},5~{R},9~{S},14~{S},15~{S},19~{S},20~{S},21~{R})-4,15,20-tris(2-azanyl-2-oxidanylidene-ethyl)-9,14,19-tris(3-azanyl-3-oxidanylidene-propyl)-5,7,10,10,15,17,20,21-octamethyl-1-(2-pyren-1-ylethynyl)-22-aza-2,23,24-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-2(6),7,11(24),12,16(23),17-hexaen-5-yl]propanoylamino]propan-2-yl hydrogen phosphate


Mass: 1555.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C80H98CoN13O14P / 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.: 564 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
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: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0972 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0972 Å / Relative weight: 1
ReflectionResolution: 1.36→41.19 Å / Num. obs: 101977 / % possible obs: 93.9 % / Redundancy: 18.1 % / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.01 / Rrim(I) all: 0.043 / Χ2: 0.99 / Net I/σ(I): 28.6 / Num. measured all: 1847253
Reflection shellResolution: 1.36→1.38 Å / % possible obs: 47.5 % / Redundancy: 8.5 % / Rmerge(I) obs: 4.399 / Num. measured all: 21776 / Num. unique obs: 2571 / CC1/2: 0.387 / Rpim(I) all: 1.578 / Rrim(I) all: 4.685 / Χ2: 0.94 / Net I/σ(I) obs: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→41.19 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 2010 1.98 %
Rwork0.1729 --
obs0.1734 101598 93.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→41.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3280 267 564 4111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063942
X-RAY DIFFRACTIONf_angle_d1.2316152
X-RAY DIFFRACTIONf_dihedral_angle_d13.5371936
X-RAY DIFFRACTIONf_chiral_restr0.057798
X-RAY DIFFRACTIONf_plane_restr0.015170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.5444730.44843846X-RAY DIFFRACTION51
1.39-1.430.39831200.39655768X-RAY DIFFRACTION75
1.43-1.470.37651440.34336858X-RAY DIFFRACTION90
1.47-1.520.32721420.27147271X-RAY DIFFRACTION96
1.52-1.580.24651440.2087480X-RAY DIFFRACTION98
1.58-1.640.2341500.17327554X-RAY DIFFRACTION99
1.64-1.710.1911460.15477528X-RAY DIFFRACTION99
1.71-1.80.20221570.16537557X-RAY DIFFRACTION99
1.8-1.920.24061500.18647587X-RAY DIFFRACTION100
1.92-2.060.21451560.18377580X-RAY DIFFRACTION100
2.06-2.270.23841520.19527580X-RAY DIFFRACTION100
2.27-2.60.21931560.19797628X-RAY DIFFRACTION100
2.6-3.280.19171550.17847617X-RAY DIFFRACTION100
3.28-41.190.1561650.13667734X-RAY DIFFRACTION100

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