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- PDB-6aso: Structure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA -

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Basic information

Entry
Database: PDB / ID: 6aso
TitleStructure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA
Components
  • (U6 snRNA-associated Sm-like protein ...) x 7
  • Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence
  • U4/U6 snRNA-associated-splicing factor PRP24
KeywordsSPLICING / Lsm2-8 spliceosome U6 Prp24
Function / homology
Function and homology information


mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / snRNA binding / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / P-body assembly / U2-type prespliceosome ...mRNA decay by 5' to 3' exoribonuclease / Lsm1-7-Pat1 complex / U6 snRNP / deadenylation-dependent decapping of nuclear-transcribed mRNA / snRNA binding / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / spliceosomal tri-snRNP complex / P-body assembly / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / spliceosomal complex assembly / nuclear-transcribed mRNA catabolic process / spliceosomal tri-snRNP complex assembly / U6 snRNA binding / spliceosomal snRNP assembly / cellular response to glucose starvation / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / maturation of SSU-rRNA / spliceosomal complex / P-body / mRNA splicing, via spliceosome / rRNA processing / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / nucleus / cytoplasm
Similarity search - Function
Occluded RNA-recognition motif / Prp24, RNA recognition motif1 / Prp24, RNA recognition motif2 / : / Occluded RNA-recognition motif / LSM-interacting domain / Lsm interaction motif / Sm-like protein Lsm8 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 ...Occluded RNA-recognition motif / Prp24, RNA recognition motif1 / Prp24, RNA recognition motif2 / : / Occluded RNA-recognition motif / LSM-interacting domain / Lsm interaction motif / Sm-like protein Lsm8 / U6 snRNA-associated Sm-like protein LSm2 / Sm-like protein Lsm4 / Sm-like protein Lsm7 / U6 snRNA-associated Sm-like protein Lsm1/8 / Sm-like protein LSm5 / Sm-like protein Lsm3 / U6 snRNA-associated Sm-like protein Lsm3 / SH3 type barrels. - #100 / Sm-like protein Lsm7/SmG / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / 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 / SH3 type barrels. / Roll / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / U6 snRNA-associated Sm-like protein LSm6 / LSM complex subunit LSM2 / LSM complex subunit LSM4 / LSM complex subunit LSM5 / LSM2-LSM8 complex subunit LSM8 ...: / : / : / RNA / RNA (> 10) / U6 snRNA-associated Sm-like protein LSm6 / LSM complex subunit LSM2 / LSM complex subunit LSM4 / LSM complex subunit LSM5 / LSM2-LSM8 complex subunit LSM8 / U4/U6 snRNA-associated-splicing factor PRP24 / LSM complex subunit LSM7 / LSM complex subunit LSM3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsMontemayor, E.J. / Brow, D.A. / Butcher, S.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118131 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM118075 United States
CitationJournal: Nat Commun / Year: 2018
Title: Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA.
Authors: Montemayor, E.J. / Didychuk, A.L. / Yake, A.D. / Sidhu, G.K. / Brow, D.A. / Butcher, S.E.
History
DepositionAug 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 21, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / reflns ...pdbx_struct_conn_angle / reflns / reflns_shell / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _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_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.ptnr2_symmetry / _struct_conn_type.id
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U4/U6 snRNA-associated-splicing factor PRP24
B: U6 snRNA-associated Sm-like protein LSm2
C: U6 snRNA-associated Sm-like protein LSm3
D: U6 snRNA-associated Sm-like protein LSm4
E: U6 snRNA-associated Sm-like protein LSm5
F: U6 snRNA-associated Sm-like protein LSm6
G: U6 snRNA-associated Sm-like protein LSm7
H: U6 snRNA-associated Sm-like protein LSm8
I: Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,37914
Polymers155,1979
Non-polymers1825
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24230 Å2
ΔGint-129 kcal/mol
Surface area50150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.197, 77.390, 118.614
Angle α, β, γ (deg.)90.00, 105.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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U6 snRNA-associated Sm-like protein ... , 7 types, 7 molecules BCDEFGH

#2: Protein U6 snRNA-associated Sm-like protein LSm2 / Small nuclear ribonucleoprotein D homolog SNP3


Mass: 11177.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM2, SMX5, SNP3, YBL026W, YBL0425 / Production host: Escherichia coli (E. coli) / References: UniProt: P38203
#3: Protein U6 snRNA-associated Sm-like protein LSm3 / SmX4 protein


Mass: 11081.407 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM3, SMX4, USS2, YLR438C-A / Production host: Escherichia coli (E. coli) / References: UniProt: P57743
#4: Protein U6 snRNA-associated Sm-like protein LSm4


Mass: 10627.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM4, SDB23, USS1, YER112W / Production host: Escherichia coli (E. coli) / References: UniProt: P40070
#5: Protein U6 snRNA-associated Sm-like protein LSm5


Mass: 10432.954 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM5, YER146W / Production host: Escherichia coli (E. coli) / References: UniProt: P40089
#6: Protein U6 snRNA-associated Sm-like protein LSm6


Mass: 9550.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YJM789 / Gene: LSM6, SCY_1265 / Production host: Escherichia coli (E. coli) / References: UniProt: A6ZYX7
#7: Protein U6 snRNA-associated Sm-like protein LSm7


Mass: 13027.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM7, YNL147W, N1202, N1780 / Production host: Escherichia coli (E. coli) / References: UniProt: P53905
#8: Protein U6 snRNA-associated Sm-like protein LSm8


Mass: 13232.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: LSM8, YJR022W, J1464, YJR83.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P47093

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Protein / RNA chain , 2 types, 2 molecules AI

#1: Protein U4/U6 snRNA-associated-splicing factor PRP24 / U4/U6 snRNP protein


Mass: 49049.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PRP24, YMR268C, YM8156.10C / Production host: Escherichia coli (E. coli) / References: UniProt: P49960
#9: RNA chain Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence


Mass: 27017.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 1039023481

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Non-polymers , 4 types, 139 molecules

#10: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#11: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 280 mM sodium potassium tartrate 22.5 % glycerol 17.5 % PEG 3,350 1 mM manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.711→90.59 Å / Num. obs: 40745 / % possible obs: 100 % / Redundancy: 60.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.446 / Rpim(I) all: 0.058 / Net I/σ(I): 8.7
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 58.5 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4574 / CC1/2: 0.418 / Rpim(I) all: 2.18 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VSU

5vsu


Resolution: 2.71→55.63 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 27.9
RfactorNum. reflection% reflection
Rfree0.247 2600 7.88 %
Rwork0.195 --
obs0.199 32994 73.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.71→55.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7223 1495 5 134 8857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118990
X-RAY DIFFRACTIONf_angle_d1.65612455
X-RAY DIFFRACTIONf_dihedral_angle_d17.9743601
X-RAY DIFFRACTIONf_chiral_restr0.0861513
X-RAY DIFFRACTIONf_plane_restr0.0111323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7106-2.75990.267380.349583X-RAY DIFFRACTION4
2.7599-2.8130.362250.278296X-RAY DIFFRACTION14
2.813-2.87040.3541540.2884616X-RAY DIFFRACTION29
2.8704-2.93280.3503660.2757787X-RAY DIFFRACTION37
2.9328-3.0010.3138820.2723987X-RAY DIFFRACTION46
3.001-3.07610.31491060.27381179X-RAY DIFFRACTION55
3.0761-3.15920.27521160.27881348X-RAY DIFFRACTION62
3.1592-3.25220.30231350.22991571X-RAY DIFFRACTION72
3.2522-3.35710.28851450.21611783X-RAY DIFFRACTION82
3.3571-3.47710.26621820.20982074X-RAY DIFFRACTION96
3.4771-3.61630.27161840.19422164X-RAY DIFFRACTION100
3.6163-3.78080.25061810.1782159X-RAY DIFFRACTION100
3.7808-3.98010.23641790.16852175X-RAY DIFFRACTION100
3.9801-4.22940.22841940.15922163X-RAY DIFFRACTION100
4.2294-4.55580.2051840.14482197X-RAY DIFFRACTION100
4.5558-5.0140.20781830.14922180X-RAY DIFFRACTION100
5.014-5.73890.22632000.18412176X-RAY DIFFRACTION100
5.7389-7.2280.29281840.23082208X-RAY DIFFRACTION99
7.228-55.64030.22411920.22832248X-RAY DIFFRACTION99
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)
10.89190.48490.20573.0412-0.93183.00140.0957-1.0565-0.17970.64780.212-0.55180.04520.971-0.05910.59980.3479-0.15351.3144-0.13220.416723.31187.158939.2833
21.89290.324-0.48593.36450.48912.71860.0574-1.53450.76280.44190.0687-0.2284-0.41550.2868-0.1880.70670.2863-0.02120.8265-0.5484-0.099210.003297.028739.1487
31.07290.30720.23842.2744-0.69621.23450.27890.0445-0.214-0.20.0497-0.03630.4806-0.6190.23141.78620.48570.05451.47751.03650.70619.099358.32950.244
43.00281.0936-0.45814.8189-1.13894.65120.0998-0.87790.12510.00050.03990.46970.6133-0.6037-0.04960.75370.03510.25971.19510.26730.6492-16.766677.078340.0474
53.32420.7048-0.6652.6528-1.76843.16850.3788-1.45350.63510.12190.47190.7946-0.542-0.35380.33930.65540.48160.12440.7714-0.0646-0.1929-7.557491.972634.4837
62.7385-0.13071.93541.28220.03391.3358-0.2841-0.584-0.32450.72620.58970.69071.1293-0.36780.06181.3264-0.19550.14071.29160.51890.8576-10.687661.74746.397
70.76360.61431.09131.98391.05451.74840.0406-0.8417-0.27840.8796-0.0392-0.65280.54150.12760.01481.11760.38220.02431.71890.21840.555516.332276.997651.4466
82.8121-1.93853.16935.5522-3.7634.16970.9028-2.7708-0.42961.4941.83432.86850.682-1.8173-1.98221.60190.36190.41972.13820.17321.459643.005959.980630.6847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'B' )
2X-RAY DIFFRACTION2(CHAIN 'C' )
3X-RAY DIFFRACTION3(CHAIN 'D' )
4X-RAY DIFFRACTION4(CHAIN 'E' )
5X-RAY DIFFRACTION5(CHAIN 'F' )
6X-RAY DIFFRACTION6(CHAIN 'G' )
7X-RAY DIFFRACTION7(CHAIN 'H' )
8X-RAY DIFFRACTION8(CHAIN 'I' AND ((RESSEQ 33:38))) OR (CHAIN 'I' AND ((RESSEQ 93:98)))

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