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- PDB-5ddo: Structural and Dynamic Basis for Low Affinity-High Selectivity Bi... -

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Basic information

Entry
Database: PDB / ID: 5ddo
TitleStructural and Dynamic Basis for Low Affinity-High Selectivity Binding of L-glutamine by the Gln-riboswitch
Components
  • L-glutamine riboswitch (58-MER)
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN/RNA / riboswitch / L-glutamine / free-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
RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Synechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRen, A. / Patel, D.
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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-glutamine riboswitch (58-MER)
G: U1 small nuclear ribonucleoprotein A
B: L-glutamine riboswitch (58-MER)
C: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)61,8564
Polymers61,8564
Non-polymers00
Water19811
1
A: L-glutamine riboswitch (58-MER)
G: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)30,9282
Polymers30,9282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-4 kcal/mol
Surface area13640 Å2
MethodPISA
2
B: L-glutamine riboswitch (58-MER)
C: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)30,9282
Polymers30,9282
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-5 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.840, 99.652, 88.461
Angle α, β, γ (deg.)90.00, 99.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain L-glutamine riboswitch (58-MER)


Mass: 19718.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: some nucleotides are too flexible in the structure / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2 M Na-formate, 21% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 12813 / % possible obs: 99.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Net I/av σ(I): 15.7 / Net I/σ(I): 15.7
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: U1A protein

Resolution: 3.1→39.917 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2887 624 4.88 %
Rwork0.2274 --
obs0.2305 12791 98.92 %
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.469 Å2 / ksol: 0.241 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--22.0276 Å20 Å2-11.0795 Å2
2--17.3009 Å2-0 Å2
3---4.7267 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 2480 0 11 3791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084095
X-RAY DIFFRACTIONf_angle_d1.2616102
X-RAY DIFFRACTIONf_dihedral_angle_d21.4081846
X-RAY DIFFRACTIONf_chiral_restr0.074787
X-RAY DIFFRACTIONf_plane_restr0.007345
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0776-3.38720.30851570.27072957X-RAY DIFFRACTION97
3.3872-3.8770.31611470.25073049X-RAY DIFFRACTION100
3.877-4.88320.31531620.21863069X-RAY DIFFRACTION100
4.8832-39.92020.25341580.2123092X-RAY DIFFRACTION99

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