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- PDB-5lr4: RNA duplex has central consecutive GA pairs flanked by G-U basepa... -

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Basic information

Entry
Database: PDB / ID: 5lr4
TitleRNA duplex has central consecutive GA pairs flanked by G-U basepairs with a methyl group on the adenine N6
ComponentsRNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
KeywordsRNA / N6-methyladenine / RNA folding / Watson-Crick basepairs / Hoogsteen-sugar edge A-G basepair
Function / homologyRNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsHuang, L. / Lilley, D.M.J.
CitationJournal: EMBO Rep. / Year: 2017
Title: Control of box C/D snoRNP assembly by N(6)-methylation of adenine.
Authors: Huang, L. / Ashraf, S. / Wang, J. / Lilley, D.M.
History
DepositionAug 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Feb 20, 2019Group: Data collection / Polymer sequence
Category: diffrn_source / entity_poly / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
B: RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
C: RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
D: RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3928
Polymers13,3004
Non-polymers924
Water1,00956
1
A: RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
B: RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6733
Polymers6,6502
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
D: RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7195
Polymers6,6502
Non-polymers693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.870, 49.870, 123.735
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: RNA chain
RNA (5'-R(*GP*(CBV)P*CP*GP*GP*(6MZ)P*UP*GP*GP*C)-3')


Mass: 3324.911 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Chloride, 0.1M Bis-Tris pH 6.5, 1.5 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9196 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 1.72→46.26 Å / Num. obs: 17404 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 11.7 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.5
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 12.2 % / Rmerge(I) obs: 2.2 / Mean I/σ(I) obs: 1 / CC1/2: 0.898 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
xia2data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→46.255 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.73
RfactorNum. reflection% reflection
Rfree0.2888 1268 4.74 %
Rwork0.2694 --
obs0.2704 14934 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→46.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 872 4 56 932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009972
X-RAY DIFFRACTIONf_angle_d4.2181524
X-RAY DIFFRACTIONf_dihedral_angle_d20.309468
X-RAY DIFFRACTIONf_chiral_restr0.06188
X-RAY DIFFRACTIONf_plane_restr0.00940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.87210.52551270.51142949X-RAY DIFFRACTION100
1.8721-1.95730.50911550.46842693X-RAY DIFFRACTION93
1.9573-2.06050.37811270.40362842X-RAY DIFFRACTION96
2.0605-2.18960.35521650.37662854X-RAY DIFFRACTION98
2.1896-2.35860.36611620.36822835X-RAY DIFFRACTION98
2.3586-2.5960.3481130.352834X-RAY DIFFRACTION96
2.596-2.97160.32041300.30312811X-RAY DIFFRACTION96
2.9716-3.74360.26241470.23622807X-RAY DIFFRACTION96
3.7436-46.27010.1961420.1672873X-RAY DIFFRACTION98
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)
17.69163.2877-5.12166.2127-2.1763.55890.2361-0.83060.31650.64930.1215-0.1151-0.54640.6427-0.32920.47920.046-0.03290.3438-0.0490.3345-4.559527.1027-1.8188
27.05255.67184.64446.45685.02374.20360.8312-0.0013-0.84220.08550.0082-0.58631.08570.0357-0.68760.88780.1217-0.26080.69810.04520.5322.227817.698113.6024
36.72590.18380.6273.32161.39865.30130.69350.6323-0.6248-0.7282-0.2778-0.0827-0.07230.0525-0.38580.6448-0.0131-0.11140.5045-0.07230.40173.509726.259411.1502
46.2088-4.96812.29558.2511-5.28113.6191-0.2049-0.399-0.1960.19410.5441-0.25170.1690.2112-0.33740.57330.0566-0.07160.2615-0.07510.3402-5.870418.2876-3.6959
52.9182-0.661-2.77718.56674.40996.42870.41560.5227-0.3109-0.9472-0.04650.2534-0.2814-1.486-0.32520.54610.0831-0.09890.5524-0.03520.3344-18.973727.8314-8.9138
60.92251.4088-0.64232.8405-0.69590.55580.7742-0.0792-1.04970.68930.3771-0.19471.26280.0964-0.09831.1682-0.2197-0.41470.6183-0.03010.6367-27.632818.0519-23.0861
72.0023-4.67340.50178.8021-1.82528.64190.9015-1.4882-0.41671.01520.0588-0.3251-0.2217-0.2646-0.74330.45960.0052-0.11470.39060.00160.3915-27.656427.7818-23.4264
81.4734-0.51660.27523.82310.72520.2338-0.0459-0.4444-0.6034-0.38550.92270.19870.7195-1.8512-0.40670.6561-0.2203-0.15330.73470.29150.3908-20.249119.8793-7.7171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:5)
2X-RAY DIFFRACTION2(chain A and resid 6:10)
3X-RAY DIFFRACTION3(chain B and resid 1:5)
4X-RAY DIFFRACTION4(chain B and resid 6:10)
5X-RAY DIFFRACTION5(chain C and resid 1:5)
6X-RAY DIFFRACTION6(chain C and resid 6:10)
7X-RAY DIFFRACTION7(chain D and resid 1:4)
8X-RAY DIFFRACTION8(chain D and resid 5:10)

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