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- PDB-6lau: the wildtype SAM-VI riboswitch bound to SAH -

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Basic information

Entry
Database: PDB / ID: 6lau
Titlethe wildtype SAM-VI riboswitch bound to SAH
Components
  • RNA (54-MER)
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA / Riboswitch / SAH / SAM-VI / 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
: / GUANOSINE-5'-TRIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Bifidobacterium angulatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.109 Å
AuthorsRen, A. / Sun, A.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870810, 91640104 and 31670826 China
CitationJournal: Nat Commun / Year: 2019
Title: SAM-VI riboswitch structure and signature for ligand discrimination.
Authors: Sun, A. / Gasser, C. / Li, F. / Chen, H. / Mair, S. / Krasheninina, O. / Micura, R. / Ren, A.
History
DepositionNov 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (54-MER)
B: RNA (54-MER)
C: U1 small nuclear ribonucleoprotein A
E: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8519
Polymers68,4265
Non-polymers1,4254
Water59433
1
A: RNA (54-MER)
E: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7615
Polymers28,7212
Non-polymers1,0403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-46 kcal/mol
Surface area12810 Å2
MethodPISA
2
B: RNA (54-MER)
C: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1053
Polymers28,7212
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-13 kcal/mol
Surface area13440 Å2
MethodPISA
3
D: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)10,9841
Polymers10,9841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.088, 85.021, 93.392
Angle α, β, γ (deg.)90.000, 105.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain / Protein , 2 types, 5 molecules ABCED

#1: RNA chain RNA (54-MER)


Mass: 17736.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bifidobacterium angulatum (bacteria)
#2: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 10984.264 Da / Num. of mol.: 3 / Mutation: Y31H, Q36R, S46K
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 , 4 types, 37 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.13 Å3/Da / Density % sol: 60.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.102 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 14922 / % possible obs: 97.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 80.37 Å2 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.061 / Rrim(I) all: 0.161 / Χ2: 0.435 / Net I/σ(I): 2.7 / Num. measured all: 100278
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.1561.1256760.6690.4921.2320.42291.5
3.15-3.216.41.0196960.6820.4371.1110.43693
3.21-3.2770.9157720.7770.3710.9890.42498.8
3.27-3.3470.8797450.7310.3550.9480.4499.7
3.34-3.4170.6987490.8430.2840.7550.41999.2
3.41-3.4970.5387660.9190.2170.5810.43399.5
3.49-3.586.90.4967430.9290.2020.5360.4499.5
3.58-3.686.90.4317500.9380.1760.4660.45899.6
3.68-3.786.90.3327670.9410.1350.3590.45599.6
3.78-3.916.80.2567460.9740.1050.2770.4599.7
3.91-4.046.80.2067660.980.0850.2230.46999.2
4.04-4.216.70.1737380.9860.0710.1880.4598.3
4.21-4.46.40.1437630.9870.0610.1560.46299.5
4.4-4.636.10.1186970.9920.0510.1290.46291.3
4.63-4.926.70.1057180.9940.0430.1130.43196.5
4.92-5.370.0967800.9950.0390.1030.42599.6
5.3-5.836.90.0887580.9950.0360.0950.42399.5
5.83-6.676.80.0757780.9970.0310.0810.409100
6.67-8.396.40.0597620.9970.0250.0640.40298.1
8.39-406.60.047520.9990.0160.0430.39594.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LAS

6las


Resolution: 3.109→39.729 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.64
RfactorNum. reflection% reflection
Rfree0.2516 707 4.75 %
Rwork0.1906 --
obs0.1937 14883 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.54 Å2 / Biso mean: 76.5707 Å2 / Biso min: 33.62 Å2
Refinement stepCycle: final / Resolution: 3.109→39.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 2329 85 33 4606
Biso mean--98.71 50.54 -
Num. residues----379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014891
X-RAY DIFFRACTIONf_angle_d1.387138
X-RAY DIFFRACTIONf_chiral_restr0.073889
X-RAY DIFFRACTIONf_plane_restr0.006489
X-RAY DIFFRACTIONf_dihedral_angle_d19.1872699
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1092-3.34910.34811260.2617269893
3.3491-3.68590.31381240.2176290499
3.6859-4.21880.22621390.1764288899
4.2188-5.31320.23761640.1719280797
5.3132-39.7290.23621540.1832287997

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