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- PDB-6chr: Crystal structure of a group II intron lariat with an intact 3' s... -

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Basic information

Entry
Database: PDB / ID: 6chr
TitleCrystal structure of a group II intron lariat with an intact 3' splice site (pre-2s state)
Components
  • RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*A)-3')
  • RNA (621-MER)
KeywordsRNA / group II intron / RNA splicing / spliceosome / lariat 3'-exon
Function / homologySPERMINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesPylaiella littoralis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.7 Å
AuthorsChan, R.T. / Peters, J.K. / Robart, A.R. / Wiryaman, T. / Rajashankar, K.R. / Toor, N.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM102216 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM123275 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5P41GM103403 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM007240 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008326 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for the second step of group II intron splicing.
Authors: Chan, R.T. / Peters, J.K. / Robart, A.R. / Wiryaman, T. / Rajashankar, K.R. / Toor, N.
History
DepositionFeb 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 (621-MER)
B: RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,63694
Polymers206,2342
Non-polymers2,40292
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: RNA sequencing performed to verify the presence of an intact 3' splice site.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-629 kcal/mol
Surface area99340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.015, 256.893, 137.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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RNA chain , 2 types, 2 molecules AB

#1: RNA chain RNA (621-MER)


Mass: 202121.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pylaiella littoralis (eukaryote)
#2: RNA chain RNA (5'-R(P*UP*GP*UP*UP*UP*AP*UP*UP*AP*AP*AP*AP*A)-3')


Mass: 4112.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pylaiella littoralis (eukaryote)

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Non-polymers , 4 types, 328 molecules

#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 82 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.54 Å3/Da / Density % sol: 65.29 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.4 mM spermine, 21% 2-Methyl-2,4-pentanediol, 175 mM magnesium acetate tetrahydrate, and 90 mM MES monohydrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.7→150 Å / Num. obs: 31200 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rsym value: 0.114 / Net I/σ(I): 15.1
Reflection shellResolution: 3.7→3.82 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.21 / Num. unique obs: 2986 / Rsym value: 0.586 / % possible all: 92.9

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.7→50.077 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.39
RfactorNum. reflection% reflection
Rfree0.2529 1511 4.84 %
Rwork0.2173 --
obs0.2191 31200 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.7→50.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 13543 336 5 13884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215406
X-RAY DIFFRACTIONf_angle_d0.51524202
X-RAY DIFFRACTIONf_dihedral_angle_d18.0937598
X-RAY DIFFRACTIONf_chiral_restr0.0343164
X-RAY DIFFRACTIONf_plane_restr0.002632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-3.81950.33811310.32372580X-RAY DIFFRACTION96
3.8195-3.95590.32531340.30682639X-RAY DIFFRACTION99
3.9559-4.11430.27681350.27412670X-RAY DIFFRACTION99
4.1143-4.30140.26141360.262679X-RAY DIFFRACTION100
4.3014-4.52810.3131370.25982687X-RAY DIFFRACTION100
4.5281-4.81150.25871370.2572702X-RAY DIFFRACTION100
4.8115-5.18270.2831380.24642701X-RAY DIFFRACTION100
5.1827-5.70360.28521390.23832723X-RAY DIFFRACTION99
5.7036-6.52740.2751380.24722716X-RAY DIFFRACTION100
6.5274-8.21790.28021410.22912752X-RAY DIFFRACTION99
8.2179-50.08160.19921450.15732840X-RAY DIFFRACTION99

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