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- PDB-9e5k: env2 cobalamin riboswitch aptamer domain in complex with ethynyl-... -

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Basic information

Entry
Database: PDB / ID: 9e5k
Titleenv2 cobalamin riboswitch aptamer domain in complex with ethynyl-3-methylbenzene-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: 1.9 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

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Assembly

Deposited unit
A: RNA (76-MER)
B: RNA (76-MER)
C: RNA (76-MER)
D: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,58156
Polymers98,9274
Non-polymers7,65552
Water13,836768
1
A: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,64514
Polymers24,7321
Non-polymers1,91413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,64514
Polymers24,7321
Non-polymers1,91413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,64514
Polymers24,7321
Non-polymers1,91413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,64514
Polymers24,7321
Non-polymers1,91413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.091, 78.659, 80.217
Angle α, β, γ (deg.)89.99, 90.03, 90.03
Int Tables number1
Space group name H-MP1

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Components

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RNA chain , 1 types, 4 molecules ABCD

#1: RNA chain
RNA (76-MER)


Mass: 24731.697 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) marine metagenome (others)

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Non-polymers , 6 types, 820 molecules

#2: Chemical
ChemComp-A1BER / ethynyl-3-methylbenzene-cobalamin / [(2~{R},3~{S},4~{R},5~{S})-5-(5,6-dimethylbenzimidazol-1-yl)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] [(2~{R})-1-[3-[(3~{R},4~{R},5~{R},9~{S},11~{S},13~{R},14~{S},15~{S},17~{S},18~{R},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-(3-methylphenyl)ethynyl]-2,22,23,24-tetraza-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}]tetracos-6-en-5-yl]propanoylamino]propan-2-yl] hydrogen phosphate


Mass: 1445.508 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C71H96CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-N3D / N-methylpropane-1,3-diamine


Mass: 88.151 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
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: 1.9→20 Å / Num. obs: 74996 / % possible obs: 95.2 % / Redundancy: 10.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.033 / Rrim(I) all: 0.11 / Χ2: 0.99 / Net I/σ(I): 21.8 / Num. measured all: 3704199
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 91.7 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.1 / Num. measured all: 181059 / Num. unique obs: 6783 / CC1/2: 0.931 / Rpim(I) all: 0.186 / Rrim(I) all: 0.585 / Χ2: 0.95 / Net I/σ(I) obs: 0.3 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.91 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 1980 2.64 %
Rwork0.1909 --
obs0.1917 74954 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6560 496 768 7824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097836
X-RAY DIFFRACTIONf_angle_d1.6612224
X-RAY DIFFRACTIONf_dihedral_angle_d16.3433816
X-RAY DIFFRACTIONf_chiral_restr0.0831532
X-RAY DIFFRACTIONf_plane_restr0.014316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.341200.29884416X-RAY DIFFRACTION80
1.95-20.32731450.28744838X-RAY DIFFRACTION89
2-2.060.33881360.27925301X-RAY DIFFRACTION94
2.06-2.130.31711400.25825162X-RAY DIFFRACTION95
2.13-2.20.26071540.23635224X-RAY DIFFRACTION96
2.2-2.290.27431370.2285379X-RAY DIFFRACTION96
2.29-2.390.29091420.22275188X-RAY DIFFRACTION95
2.39-2.520.31961410.24785137X-RAY DIFFRACTION94
2.52-2.680.30261400.25125361X-RAY DIFFRACTION97
2.68-2.880.32121510.23895354X-RAY DIFFRACTION98
2.88-3.170.2741510.2045393X-RAY DIFFRACTION98
3.17-3.630.20771610.17285347X-RAY DIFFRACTION98
3.63-4.560.15661310.15275426X-RAY DIFFRACTION98
4.56-19.910.13591310.14065448X-RAY DIFFRACTION99

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