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- PDB-37cn: env2 cobalamin riboswitch aptamer domain in complex with ethynyl-... -

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Basic information

Entry
Database: PDB / ID: 37cn
Titleenv2 cobalamin riboswitch aptamer domain in complex with ethynyl-N-cyclopentylpropiolamide-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: 2.99 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: To Be Published
Title: Reimagining productive chemical space for RNA recognition beyond aromaticity
Authors: Olenginski, L.T. / Batey, R.T.
History
DepositionJul 14, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 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 (76-MER)
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,98827
Polymers49,1432
Non-polymers3,84525
Water543
1
A: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,50614
Polymers24,5721
Non-polymers1,93513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,48213
Polymers24,5721
Non-polymers1,91012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.686, 76.533, 73.550
Angle α, β, γ (deg.)90.00, 90.91, 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: 24571.738 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) marine metagenome (others)

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Non-polymers , 6 types, 28 molecules

#2: Chemical ChemComp-A1DMT / ethynyl-N-cyclopentylpropiolamide-cobalamin


Mass: 1466.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C70H99CoN14O15P / 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.: 17 / 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.: 3 / 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: 2.59 Å3/Da / Density % sol: 52.42 %
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: Mar 13, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 15720 / % possible obs: 94.9 % / Redundancy: 2.4 % / Rpim(I) all: 0.074 / Rrim(I) all: 0.125 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.591.70.22412900.940.9850.1850.2920.62779.4
2.59-2.692.10.21615260.9480.9870.170.2760.66792.8
2.69-2.812.40.19716030.9620.990.1450.2460.82996.2
2.81-2.962.50.16116010.970.9920.1190.2011.11198.2
2.96-3.152.50.1715990.9510.9870.1260.2121.79198.1
3.15-3.392.50.12316440.9830.9960.0920.1542.14497.8
3.39-3.732.60.10116050.9850.9960.0740.1262.16397.5
3.73-4.262.50.08816400.9850.9960.0660.112.26497
4.26-5.352.60.07315980.9870.9970.0530.0912.15796.6
5.35-202.40.0616140.9890.9970.0450.0752.31895.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→19.72 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2972 930 10.19 %
Rwork0.2005 --
obs0.2104 9127 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.99→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3262 249 3 3514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013906
X-RAY DIFFRACTIONf_angle_d1.816102
X-RAY DIFFRACTIONf_dihedral_angle_d16.6661950
X-RAY DIFFRACTIONf_chiral_restr0.078790
X-RAY DIFFRACTIONf_plane_restr0.01170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.150.4111280.33071144X-RAY DIFFRACTION93
3.15-3.340.34211330.23491159X-RAY DIFFRACTION93
3.34-3.60.31991290.20561173X-RAY DIFFRACTION95
3.6-3.960.27931420.17451153X-RAY DIFFRACTION94
3.96-4.530.2661290.16031176X-RAY DIFFRACTION95
4.53-5.680.23551320.15171198X-RAY DIFFRACTION96
5.68-19.720.26911370.19851194X-RAY DIFFRACTION95

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