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- PDB-5ddq: L-glutamine riboswitch bound with L-glutamine soaked with Mn2+ -

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Basic information

Entry
Database: PDB / ID: 5ddq
TitleL-glutamine riboswitch bound with L-glutamine soaked with Mn2+
Components
  • L-glutamine riboswitch RNA (61-MER)
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN/RNA / riboswitch / L-glutamine / bound-form / RNA / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / : / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Synechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsRen, A. / Patel, D.J.
CitationJournal: Cell Rep / Year: 2015
Title: Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.
Authors: Ren, A. / Xue, Y. / Peselis, A. / Serganov, A. / Al-Hashimi, H.M. / Patel, D.J.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Derived calculations
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-glutamine riboswitch RNA (61-MER)
B: L-glutamine riboswitch RNA (61-MER)
C: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,81626
Polymers61,9004
Non-polymers91622
Water3,891216
1
A: L-glutamine riboswitch RNA (61-MER)
D: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,44614
Polymers30,9502
Non-polymers49612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-102 kcal/mol
Surface area14210 Å2
MethodPISA
2
B: L-glutamine riboswitch RNA (61-MER)
C: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,37012
Polymers30,9502
Non-polymers42010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-93 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.605, 85.701, 60.889
Angle α, β, γ (deg.)90.00, 99.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain / Protein , 2 types, 4 molecules ABCD

#1: RNA chain L-glutamine riboswitch RNA (61-MER)


Mass: 19740.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechococcus elongatus (bacteria)
#2: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 11209.120 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: Escherichia coli (E. coli) / References: UniProt: P09012

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Non-polymers , 5 types, 238 molecules

#3: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O3
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1 M HEPES-sodium, pH 7.0, 40% (v/v) 2-methyl-2,4-pentanediol, 2 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: FILM / Date: May 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / % possible obs: 85.8 % / Redundancy: 3.5 % / Net I/σ(I): 16.7

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.4→25.772 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 3470 9.33 %
Rwork0.1969 --
obs0.2026 37211 78.09 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.555 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.2569 Å20 Å2-4.4136 Å2
2--5.6438 Å2-0 Å2
3---1.613 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 2614 40 216 4384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024560
X-RAY DIFFRACTIONf_angle_d0.9666791
X-RAY DIFFRACTIONf_dihedral_angle_d15.3952062
X-RAY DIFFRACTIONf_chiral_restr0.068839
X-RAY DIFFRACTIONf_plane_restr0.006388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3925-2.42520.42091320.37491271X-RAY DIFFRACTION72
2.4252-2.45980.37211270.32341292X-RAY DIFFRACTION77
2.4598-2.49650.35791330.32241319X-RAY DIFFRACTION76
2.4965-2.53550.38751360.32221368X-RAY DIFFRACTION78
2.5355-2.5770.39611340.33731351X-RAY DIFFRACTION79
2.577-2.62140.41731360.3261317X-RAY DIFFRACTION76
2.6214-2.6690.35761370.3211294X-RAY DIFFRACTION76
2.669-2.72030.39151380.31831349X-RAY DIFFRACTION78
2.7203-2.77580.38571480.28411343X-RAY DIFFRACTION77
2.7758-2.83610.39141380.29131372X-RAY DIFFRACTION79
2.8361-2.9020.32311570.27271333X-RAY DIFFRACTION77
2.902-2.97440.36111400.241313X-RAY DIFFRACTION79
2.9744-3.05470.30911380.21771395X-RAY DIFFRACTION79
3.0547-3.14450.25631280.19031344X-RAY DIFFRACTION78
3.1445-3.24580.27051480.19551351X-RAY DIFFRACTION78
3.2458-3.36150.26041280.18381370X-RAY DIFFRACTION79
3.3615-3.49580.23021350.19571358X-RAY DIFFRACTION79
3.4958-3.65450.27791440.16771379X-RAY DIFFRACTION80
3.6545-3.84660.21861330.16641367X-RAY DIFFRACTION78
3.8466-4.08670.18191530.14171361X-RAY DIFFRACTION79
4.0867-4.40080.17751540.12891369X-RAY DIFFRACTION80
4.4008-4.8410.20481280.12631384X-RAY DIFFRACTION80
4.841-5.53550.14951370.12911388X-RAY DIFFRACTION79
5.5355-6.95140.19781430.16441407X-RAY DIFFRACTION81
6.9514-25.7730.24471450.18341346X-RAY DIFFRACTION79

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