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- PDB-3p49: Crystal Structure of a Glycine Riboswitch from Fusobacterium nucleatum -

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Basic information

Entry
Database: PDB / ID: 3p49
TitleCrystal Structure of a Glycine Riboswitch from Fusobacterium nucleatum
Components
  • GLYCINE RIBOSWITCH
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN/RNA / riboswitch / RNA / cooperative / glycine / 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
GLYCINE / : / RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesFusobacterium nucleatum subsp. polymorphum (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.55 Å
AuthorsButler, E.B. / Wang, J. / Xiong, Y. / Strobel, S.
CitationJournal: Chem.Biol. / Year: 2011
Title: Structural basis of cooperative ligand binding by the glycine riboswitch.
Authors: Butler, E.B. / Xiong, Y. / Wang, J. / Strobel, S.A.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 24, 2015Group: Derived calculations
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.src_method / _entity_name_com.name ..._entity.src_method / _entity_name_com.name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 1.4Feb 21, 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 / struct_site
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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCINE RIBOSWITCH
B: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,46317
Polymers65,9972
Non-polymers46615
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.580, 104.617, 156.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain GLYCINE RIBOSWITCH /


Mass: 54656.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum subsp. polymorphum (bacteria)
Description: in vitro synthesis from a plasmid DNA with T7 RNA polymerase
References: GenBank: CP013328.1
#2: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 11340.315 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN (UNP RESIDUES 1-98) / Mutation: Y31H Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P09012
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS A CHIMERA SEQUENCE IN WHICH THE P2 LOOP HAS BEEN REPLACED BY U1A BINDING LOOP

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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: 3.39 Å3/Da / Density % sol: 63.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEGmme550, 0.05M HEPES PH 7.0, 0.01M MgCL2, 0.025M NaOAC pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.0809
SYNCHROTRONAPS 24-ID-C21.1056, 1.1061, 1.0762
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 1, 2007
MAR 300 CCD2CCDJan 1, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.08091
21.10561
31.10611
41.07621
ReflectionResolution: 3.55→99 Å / Num. all: 11496 / Num. obs: 11450 / % possible obs: 99.6 % / Observed criterion σ(I): 1.645 / Redundancy: 9.1 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 13.55
Reflection shellResolution: 3.55→3.68 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 1.645 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.55→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R Free: 0.715
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30958 543 4.8 %RANDOM
Rwork0.28237 ---
obs0.28362 10796 99.94 %-
all-10803 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 222.648 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å20 Å20 Å2
2--1.31 Å20 Å2
3----3.38 Å2
Refinement stepCycle: LAST / Resolution: 3.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms749 3624 23 20 4416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214842
X-RAY DIFFRACTIONr_bond_other_d00.021947
X-RAY DIFFRACTIONr_angle_refined_deg1.3142.8577375
X-RAY DIFFRACTIONr_angle_other_deg2.35934978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.413591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.72923.23534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84815154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.524156
X-RAY DIFFRACTIONr_chiral_restr0.0560.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022589
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02532
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3141.5467
X-RAY DIFFRACTIONr_mcbond_other0.0031.5187
X-RAY DIFFRACTIONr_mcangle_it2.2932752
X-RAY DIFFRACTIONr_scbond_it2.00434375
X-RAY DIFFRACTIONr_scangle_it3.5134.56623
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.55→3.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.49 46 -
Rwork0.46 760 -
obs--99.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.831-1.3693-0.78222.6533-1.56572.8761-0.16780.12140.3443-0.07260.0188-0.0582-0.27450.15230.1490.7146-0.02420.06750.4447-0.00620.648856.459613.298639.9238
22.0715-1.2004-1.31273.7045-0.11541.7843-0.01280.3183-0.0503-0.09810.0036-0.11630.07090.30570.00920.5613-0.03020.08580.54190.03450.510658.074120.756546.6558
30.7460.9987-0.89555.1038-0.39214.39520.111-0.261-0.20940.5465-0.10870.50840.3498-0.6106-0.00220.44940.0799-0.09840.55750.11760.446840.838313.564871.4753
40.36740.23760.45550.65220.92972.5185-0.01410.2673-0.3218-0.21050.0435-0.15710.38090.2864-0.02940.5249-0.02240.04030.4930.02350.594855.69173.657351.6024
52.90440.02070.20941.80060.41242.08470.0726-0.52910.2230.5165-0.07390.2896-0.1625-0.22920.00140.51050.01380.00120.4890.00430.489823.799-1.68728.4881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 25
2X-RAY DIFFRACTION2A26 - 76
3X-RAY DIFFRACTION3A77 - 111
4X-RAY DIFFRACTION4A112 - 734
5X-RAY DIFFRACTION5B6 - 97

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