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- PDB-6laz: the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1 -

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Basic information

Entry
Database: PDB / ID: 6laz
Titlethe wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1
Components
  • RNA (55-MER)
  • U1 small nuclear ribonucleoprotein A
KeywordsRNA / Riboswitch / SAM / SAM-VI
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
Chem-E7X / 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: 2.76 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (55-MER)
B: RNA (55-MER)
C: U1 small nuclear ribonucleoprotein A
D: U1 small nuclear ribonucleoprotein A
E: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0308
Polymers68,1835
Non-polymers8473
Water32418
1
A: RNA (55-MER)
E: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1294
Polymers28,6932
Non-polymers4362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-20 kcal/mol
Surface area13320 Å2
MethodPISA
2
B: RNA (55-MER)
C: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1053
Polymers28,6932
Non-polymers4111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-12 kcal/mol
Surface area13420 Å2
MethodPISA
3
D: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)10,7971
Polymers10,7971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.390, 85.348, 93.165
Angle α, β, γ (deg.)90.000, 105.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (55-MER)


Mass: 17896.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bifidobacterium angulatum (bacteria)
#2: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 10796.682 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-E7X / (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-hydroxyethyl)amino]-2-azaniumyl-butanoate


Mass: 411.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N7O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
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: 3.17 Å3/Da / Density % sol: 61.19 %
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: BL17U1 / Wavelength: 1.102 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 2.76→42.67 Å / Num. obs: 20968 / % possible obs: 94.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 73.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.031 / Rrim(I) all: 0.081 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.76-2.96.90.7042118830510.8850.2850.7612.695.4
8.71-42.676.50.04646657220.9980.0190.0533.497.7

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Processing

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

6las


Resolution: 2.76→42.67 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.38
RfactorNum. reflection% reflection
Rfree0.2234 984 4.7 %
Rwork0.188 --
obs0.1897 20945 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 167.21 Å2 / Biso mean: 79.1927 Å2 / Biso min: 42.83 Å2
Refinement stepCycle: final / Resolution: 2.76→42.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 2368 59 18 4618
Biso mean--85.2 64.85 -
Num. residues----381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084922
X-RAY DIFFRACTIONf_angle_d1.1817175
X-RAY DIFFRACTIONf_chiral_restr0.062890
X-RAY DIFFRACTIONf_plane_restr0.006488
X-RAY DIFFRACTIONf_dihedral_angle_d19.7392702
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.76-2.90090.32831540.2819281195
2.9009-3.08260.34881370.2583298799
3.0826-3.32050.26411430.2197300099
3.3205-3.65450.25561010.2106258187
3.6545-4.18290.23331260.1846260291
4.1829-5.26850.19511560.1645302199
5.2685-42.670.18911670.1662295997

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