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- PDB-6svs: Crystal Structure of U:A-U-rich RNA triple helix with 11 consecut... -

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Basic information

Entry
Database: PDB / ID: 6svs
TitleCrystal Structure of U:A-U-rich RNA triple helix with 11 consecutive base triples
ComponentsRNA (79-mer)
KeywordsRNA / RNA triple helix poly(U:A-U) base triple
Function / homologyADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRuszkowska, A. / Ruszkowski, M. / Hulewicz, J.P. / Dauter, Z. / Brown, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM111430 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Molecular structure of a U•A-U-rich RNA triple helix with 11 consecutive base triples.
Authors: Ruszkowska, A. / Ruszkowski, M. / Hulewicz, J.P. / Dauter, Z. / Brown, J.A.
History
DepositionSep 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (79-mer)
B: RNA (79-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,57716
Polymers49,2072
Non-polymers2,37014
Water905
1
A: RNA (79-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7888
Polymers24,6031
Non-polymers1,1857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (79-mer)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7888
Polymers24,6031
Non-polymers1,1857
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.716, 78.114, 84.018
Angle α, β, γ (deg.)90.000, 104.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain RNA (79-mer)


Mass: 24603.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 19 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-A23 / ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE


Type: RNA linking / Mass: 409.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O9P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.44 Å3/Da / Density % sol: 64.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: The crystallization drop included 1.5 ul of MALAT1_th11 RNA and 1 ul reservoir solution containing 50 mM sodium cacodylate pH 6.0-6.3, 200 mM calcium acetate, and 2.5 M sodium chloride. ...Details: The crystallization drop included 1.5 ul of MALAT1_th11 RNA and 1 ul reservoir solution containing 50 mM sodium cacodylate pH 6.0-6.3, 200 mM calcium acetate, and 2.5 M sodium chloride. Crystals were cryoprotected by stepwise addition of crystallization solution supplemented with glycerol until the final concentration of 20% glycerol was reached.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40.7 Å / Num. obs: 13040 / % possible obs: 54.4 % / Redundancy: 3.9 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.045 / Net I/σ(I): 17.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.71.471.16640.41.6613
8.34-40.70.02540.964810.02995.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4plx

4plx


Resolution: 2.5→40.7 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.36
RfactorNum. reflection% reflection
Rfree0.2134 633 4.87 %
Rwork0.1666 --
obs0.1689 13011 54.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 191.72 Å2 / Biso mean: 91.9588 Å2 / Biso min: 32.23 Å2
Refinement stepCycle: final / Resolution: 2.5→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3372 20 5 3397
Biso mean--78.58 59.75 -
Num. residues----158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONbonds0.0053774
X-RAY DIFFRACTIONangles0.9125880
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.69040.468310.435354912
2.6904-2.96110.3433560.3087117726
2.9611-3.38940.23371210.1858239952
3.3894-4.26950.21021970.1752371182
4.2695-40.70.20082280.1472454298
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)
10.84970.7639-0.62311.9361-1.04930.6564-0.0557-0.22740.2256-0.2917-0.10830.5670.405-0.55250.08690.426-0.2280.04320.8149-0.17470.6336-0.1232.707911.083
24.12031.84090.04670.86030.04750.00880.0734-0.9879-0.69680.13570.2032-0.34690.2687-0.3638-0.16540.3052-0.25650.02261.29710.07170.7676-25.050125.893421.2077
33.92991.4057-1.87343.3204-1.29731.76290.03090.1440.3552-0.7892-0.35090.2156-0.0014-0.74050.02130.3679-0.07320.07070.582-0.11990.45269.105540.14224.4485
44.2141-2.1372-5.17631.71432.65056.38670.3432-0.40060.9110.14270.32010.3107-0.4157-1.0776-0.58250.94960.05650.40621.34470.06420.84736.24140.897122.4421
50.0678-0.0603-0.18550.05010.15810.50170.56051.33711.4072-0.5701-0.214-0.2495-0.6886-0.6022-0.84910.7120.53410.44851.75740.69590.9439-23.23584.790346.3654
63.9675-1.2968-2.23742.50431.01633.54320.1581-0.47590.4340.2360.21760.2705-0.1056-0.9023-0.26720.91750.03220.35950.9140.14320.711612.567-3.196919.4441
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )A2 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 46 )A22 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 78 )A47 - 78
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 21 )B2 - 21
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 36 )B22 - 36
6X-RAY DIFFRACTION6chain 'B' and (resid 37 through 78 )B37 - 78

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