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- PDB-5ddr: L-glutamine riboswitch bound with L-glutamine soaked with Cs+ -

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Basic information

Entry
Database: PDB / ID: 5ddr
TitleL-glutamine riboswitch bound with L-glutamine soaked with Cs+
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: 2.605 Å
AuthorsRen, A. / Patel, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 U19 CA179564 United States
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 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_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)63,75635
Polymers61,9004
Non-polymers1,85631
Water4,450247
1
A: L-glutamine riboswitch RNA (61-MER)
D: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,79716
Polymers30,9502
Non-polymers84714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-184 kcal/mol
Surface area14310 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)31,95819
Polymers30,9502
Non-polymers1,00917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-231 kcal/mol
Surface area14500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.967, 86.882, 62.218
Angle α, β, γ (deg.)90.00, 102.61, 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 , 6 types, 278 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cs
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 293 K / Method: evaporation
Details: .1 M HEPES-sodium, pH 7.0, 40% (v/v) 2-methyl-2,4-pentanediol, 20 mM CsCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: CCD / Date: May 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / % possible obs: 93.7 % / Redundancy: 3.3 % / Net I/σ(I): 13.4

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.605→29.368 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 3174 10.02 %
Rwork0.2116 --
obs0.2175 31684 83.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.631 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1074 Å20 Å2-0.9568 Å2
2---2.4806 Å2-0 Å2
3---6.588 Å2
Refinement stepCycle: LAST / Resolution: 2.605→29.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 2614 49 247 4419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0274580
X-RAY DIFFRACTIONf_angle_d1.1166815
X-RAY DIFFRACTIONf_dihedral_angle_d16.2582055
X-RAY DIFFRACTIONf_chiral_restr0.07840
X-RAY DIFFRACTIONf_plane_restr0.007386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6048-2.64360.54531420.49821182X-RAY DIFFRACTION80
2.6436-2.68490.4651410.41151211X-RAY DIFFRACTION82
2.6849-2.72890.43671340.37341177X-RAY DIFFRACTION80
2.7289-2.77590.37811370.35341275X-RAY DIFFRACTION85
2.7759-2.82630.38441340.33211235X-RAY DIFFRACTION82
2.8263-2.88070.41791510.31791228X-RAY DIFFRACTION84
2.8807-2.93940.35621230.29671234X-RAY DIFFRACTION81
2.9394-3.00330.41281290.25961213X-RAY DIFFRACTION83
3.0033-3.07310.33351590.22771275X-RAY DIFFRACTION84
3.0731-3.14980.31541120.21271232X-RAY DIFFRACTION83
3.1498-3.23490.3081370.21881289X-RAY DIFFRACTION83
3.2349-3.32990.26541430.20231228X-RAY DIFFRACTION83
3.3299-3.43730.2511440.21661218X-RAY DIFFRACTION82
3.4373-3.55990.28911410.20071236X-RAY DIFFRACTION84
3.5599-3.70220.28691310.19321237X-RAY DIFFRACTION83
3.7022-3.87030.29231360.18731245X-RAY DIFFRACTION83
3.8703-4.07390.21951350.17071250X-RAY DIFFRACTION84
4.0739-4.32840.2111380.17181268X-RAY DIFFRACTION85
4.3284-4.66140.21271460.17071248X-RAY DIFFRACTION85
4.6614-5.12820.23841360.15551266X-RAY DIFFRACTION83
5.1282-5.86510.15761490.1531241X-RAY DIFFRACTION84
5.8651-7.37010.20891360.18531280X-RAY DIFFRACTION86
7.3701-29.36940.20621400.19561242X-RAY DIFFRACTION83

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