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- PDB-5i8q: S. cerevisiae Prp43 in complex with RNA and ADPNP -

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Basic information

Entry
Database: PDB / ID: 5i8q
TitleS. cerevisiae Prp43 in complex with RNA and ADPNP
Components
  • Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE / helicase / RNA / unwinding
Function / homology
Function and homology information


spliceosomal complex disassembly / post-mRNA release spliceosomal complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / small-subunit processome / helicase activity ...spliceosomal complex disassembly / post-mRNA release spliceosomal complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / small-subunit processome / helicase activity / spliceosomal complex / rRNA processing / RNA helicase activity / RNA helicase / mRNA binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / ATP binding
Similarity search - Function
DHX15, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. ...DHX15, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA / RNA (> 10) / Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsHe, Y. / Nielsen, K.H. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish National Research FoundationmRNP biogenesis & metabolism Denmark
CitationJournal: RNA / Year: 2017
Title: Structure of the DEAH/RHA ATPase Prp43p bound to RNA implicates a pair of hairpins and motif Va in translocation along RNA.
Authors: He, Y. / Staley, J.P. / Andersen, G.R. / Nielsen, K.H.
History
DepositionFeb 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 2.0Aug 9, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / diffrn_source / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conf / struct_conn / struct_ref_seq / struct_sheet_range / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
B: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
F: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,0728
Polymers182,0114
Non-polymers1,0614
Water0
1
A: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
C: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9244
Polymers90,3932
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-34 kcal/mol
Surface area34380 Å2
MethodPISA
2
B: Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
F: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1484
Polymers91,6182
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-42 kcal/mol
Surface area34480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.063, 154.031, 78.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain 'B' and (resseq 41:269 ))
211(chain 'A' and (resseq 41:269 ))
112(chain 'B' and (resseq 800:1000))
212(chain 'A' and (resseq 800:1000))
113(chain 'B' and (resseq 270:452 ))
213(chain 'A' and (resseq 270:452 ))
114(chain 'B' and (resseq 4:40))
214(chain 'A' and (resseq 4:40))
115(chain 'B' and resseq 453:634)
215(chain 'A' and resseq 453:634)
116(chain 'B' and resseq 635:755)
216(chain 'A' and resseq 635:755)
117(chain 'F' and resseq 1:9)
217(chain 'C' and resseq 1:9)

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP43 / Helicase JA1


Mass: 87682.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P53131, RNA helicase
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2710.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3935.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#4: Chemical ChemComp-MG / MAGNESIUM ION / Helicase JA1


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: RNA helicase
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Helicase JA1


Mass: 506.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H17N6O12P3 / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: RNA helicase / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 292 K / Method: microbatch
Details: Crystallization buffer was prepared by mixing a solution containing 100 mM MES-NaOH, pH 6.0, 100 mM NaOAc, 8% PEG 10K and an additive solution (20% acetonitrile, 5% n-Dodecyl-?-D-maltoside) ...Details: Crystallization buffer was prepared by mixing a solution containing 100 mM MES-NaOH, pH 6.0, 100 mM NaOAc, 8% PEG 10K and an additive solution (20% acetonitrile, 5% n-Dodecyl-?-D-maltoside) in a 5:1 (v:v).Microbatch drops were formed by mixing 1.8 ?l of the crystallization buffer with 1.2 ?l of the preformed complex

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.2→30 Å / Num. obs: 15735 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.05 % / Biso Wilson estimate: 121.22 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.255 / Net I/σ(I): 8.67
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
4.2-4.341.0542.08199.9
4.34-4.490.8472.63199.9
4.49-4.670.6713.211100
4.67-4.880.6273.51100
4.88-5.140.5423.97199.9
5.14-5.460.5124.091100
5.46-5.870.4574.64199.9
5.87-6.460.3615.69199.9
6.46-7.380.2118.921100
7.38-9.250.08419.461100
9.250.03834.24195.7

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KX2

3kx2


Resolution: 4.2→29.446 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2861 1573 10.15 %
Rwork0.2603 --
obs0.2629 15493 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.2→29.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12164 434 0 0 12598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212906
X-RAY DIFFRACTIONf_angle_d0.56717562
X-RAY DIFFRACTIONf_dihedral_angle_d13.5725024
X-RAY DIFFRACTIONf_chiral_restr0.0231962
X-RAY DIFFRACTIONf_plane_restr0.0032220
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1839X-RAY DIFFRACTIONPOSITIONAL
12A1839X-RAY DIFFRACTIONPOSITIONAL0.002
21B32X-RAY DIFFRACTIONPOSITIONAL
22A32X-RAY DIFFRACTIONPOSITIONAL0.002
31B1456X-RAY DIFFRACTIONPOSITIONAL
32A1456X-RAY DIFFRACTIONPOSITIONAL0.004
41B295X-RAY DIFFRACTIONPOSITIONAL
42A295X-RAY DIFFRACTIONPOSITIONAL0.004
51B1468X-RAY DIFFRACTIONPOSITIONAL
52A1468X-RAY DIFFRACTIONPOSITIONAL0.003
61B992X-RAY DIFFRACTIONPOSITIONAL
62A992X-RAY DIFFRACTIONPOSITIONAL0.002
71F177X-RAY DIFFRACTIONPOSITIONAL
72C177X-RAY DIFFRACTIONPOSITIONAL0.002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2-4.33520.37911590.32551235X-RAY DIFFRACTION100
4.3352-4.48960.28751300.29671218X-RAY DIFFRACTION100
4.4896-4.66870.34231460.30631265X-RAY DIFFRACTION100
4.6687-4.88020.3531370.29641241X-RAY DIFFRACTION100
4.8802-5.13630.30111390.28451263X-RAY DIFFRACTION100
5.1363-5.45620.35111400.29871233X-RAY DIFFRACTION100
5.4562-5.87440.32061370.31221267X-RAY DIFFRACTION100
5.8744-6.45990.35271460.29451265X-RAY DIFFRACTION100
6.4599-7.38170.33021380.27281277X-RAY DIFFRACTION100
7.3817-9.25210.24041490.20421301X-RAY DIFFRACTION100
9.2521-29.44690.17881520.18681355X-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)
10.91791.37650.91474.15591.91370.98320-0.9869-0.70040.84080.0108-0.66440.43740.332401.8113-0.09190.09951.92260.46582.05256.2165-5.862828.854
23.9299-0.2903-1.35593.06470.63362.4105-0.1747-0.2189-0.6811-0.6463-0.1559-0.4780.22310.08870.00131.3931-0.13410.23151.22620.10992.033254.3531.52714.2434
35.24531.56061.11774.88991.03143.71710.0599-0.6064-0.0588-0.0828-0.1762-0.0060.2723-0.39310.0011.17590.02940.28431.10480.03231.374733.97812.619211.0325
44.0707-3.1531-2.53212.62990.92564.67490.16390.5120.9454-1.60120.0326-0.076-0.46590.04440.00041.3735-0.08240.05221.10790.01261.918928.762530.0884.8947
50.2029-0.01570.37644.25421.28810.96780.3505-1.45770.49250.674-0.2626-0.3607-0.35710.7632-0.00081.8455-0.32520.03842.8877-0.3861.634280.592743.596331.8004
64.0547-0.8004-1.93460.6186-0.40052.11150.7629-0.73331.09120.6168-0.2508-0.0146-0.2958-0.12950.02411.729-0.29160.37211.7652-0.40151.645459.658150.329318.2043
74.76110.72820.5596.989-2.40455.32620.21440.05840.1482-0.2492-0.4059-0.041-0.4279-0.19350.00890.97180.20480.18251.2072-0.20440.878671.91243.5893-1.3056
84.86450.26750.19395.12352.99494.1552-0.15920.95060.1724-1.0474-0.47491.87350.3453-1.07520.03291.44760.0660.01711.3665-0.07580.942565.220133.4004-16.5847
91.3454-0.4036-0.57473.5372.66252.025-1.69080.10870.9199-1.29591.31410.55171.6524-4.52840.01081.6596-0.15-0.21141.99780.20911.929543.0286.79838.8193
105.6316-2.17562.48031.5443-0.37771.5796-1.243-1.5593-0.5897-0.3678-1.0901-1.83210.65161.8267-1.27842.485-0.06510.97271.55250.29022.103932.7227-8.37478.4252
111.55341.48240.74973.92090.72740.38350.15572.19134.1075-1.3828-0.98791.1998-2.05612.332-0.01062.2768-0.30480.2532.13610.15272.579767.516546.53458.1254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and (resseq 41:269))
2X-RAY DIFFRACTION2(chain 'B' and (resseq 270:452 or resseq 4:40))
3X-RAY DIFFRACTION3(chain 'B' and resseq 453:634)
4X-RAY DIFFRACTION4(chain 'B' and resseq 635:754)
5X-RAY DIFFRACTION5(chain 'A' and (resseq 41:269))
6X-RAY DIFFRACTION6(chain 'A' and (resseq 270:452 or resseq 4:40))
7X-RAY DIFFRACTION7(chain 'A' and resseq 453:634)
8X-RAY DIFFRACTION8(chain 'A' and resseq 635:754)
9X-RAY DIFFRACTION9(chain 'F' and resseq 1:9)
10X-RAY DIFFRACTION10(chain 'F' and resseq 10:13)
11X-RAY DIFFRACTION11(chain 'C' and resseq 1:9)

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