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- PDB-6rm9: Crystal structure of the DEAH-box ATPase Prp2 in complex with Spp... -

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Basic information

Entry
Database: PDB / ID: 6rm9
TitleCrystal structure of the DEAH-box ATPase Prp2 in complex with Spp2 and ADP
Components
  • Putative mRNA splicing factor
  • Putative pre-mRNA splicing protein
KeywordsHYDROLASE / Prp2 / DEAH-box ATPase / G-patch / spliceosome
Function / homology
Function and homology information


catalytic step 2 spliceosome / RNA splicing / spliceosomal complex / helicase activity / mRNA splicing, via spliceosome / mRNA processing / hydrolase activity / RNA helicase / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Spp2/MOS2, G-patch domain / Pre-mRNA-splicing factor Spp2-like / G-patch domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold ...Spp2/MOS2, G-patch domain / Pre-mRNA-splicing factor Spp2-like / G-patch domain / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / 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 domain / DEAD/DEAH box helicase / RNA-binding domain superfamily / 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 / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / RNA helicase / Pre-mRNA-splicing factor
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHamann, F. / Neumann, P. / Ficner, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural analysis of the intrinsically disordered splicing factor Spp2 and its binding to the DEAH-box ATPase Prp2.
Authors: Hamann, F. / Schmitt, A. / Favretto, F. / Hofele, R. / Neumann, P. / Xiang, S. / Urlaub, H. / Zweckstetter, M. / Ficner, R.
History
DepositionMay 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / refine / struct_conn / struct_conn_type
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 / _refine.pdbx_diffrn_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative mRNA splicing factor
C: Putative pre-mRNA splicing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5319
Polymers78,6712
Non-polymers8607
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-49 kcal/mol
Surface area30140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.850, 77.420, 148.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Putative mRNA splicing factor


Mass: 73436.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0063660 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SEG4
#2: Protein/peptide Putative pre-mRNA splicing protein


Mass: 5234.946 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0071470 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SFN3

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Non-polymers , 6 types, 326 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris pH 5.5, 400 mM ammonium sulfate, 23% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.85→68.689 Å / Num. obs: 65564 / % possible obs: 99.7 % / Redundancy: 4.552 % / Biso Wilson estimate: 45.421 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.075 / Χ2: 1.011 / Net I/σ(I): 11.45 / Num. measured all: 298478 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.954.5311.0991.8442737945194320.6781.24599.8
1.95-2.054.6170.6353.0935720774377360.8290.71799.9
2.05-2.154.7220.4174.4330065637663670.9150.47199.9
2.15-2.254.6130.3145.7324338528552760.9280.35799.8
2.25-2.54.510.2138.2644333986198290.9580.24399.7
2.5-2.74.7470.13911.9525891546154540.9830.15799.9
2.7-34.5210.0831625966576457440.9920.09599.7
3-3.54.5650.05522.0726080574157130.9960.06299.5
3.5-4.24.4640.04427.2818396415041210.9970.04999.3
4.2-54.2010.04228.639842235623430.9970.04799.4
5-64.5010.04130.156599147414660.9970.04799.5
6-84.210.03930.124884117511600.9980.04598.7
8-103.7660.03729.4916424394360.9970.04299.3
10-204.2570.04531.6717884224200.9960.05199.5
20-503.0650.04525.7619066620.9960.05393.9
50-68.6891.40.6194.867550.876100

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6fa5

6fa5


Resolution: 1.85→68.689 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.6
RfactorNum. reflection% reflection
Rfree0.212 3278 5 %
Rwork0.1979 --
obs0.1986 65546 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 127.67 Å2 / Biso mean: 49.1824 Å2 / Biso min: 22.42 Å2
Refinement stepCycle: final / Resolution: 1.85→68.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 61 319 5778
Biso mean--48.73 50.51 -
Num. residues----695
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8499-1.87750.36021410.34932669281099
1.8775-1.90690.33841400.337726672807100
1.9069-1.93810.35661420.334626992841100
1.9381-1.97160.36381390.309626272766100
1.9716-2.00740.31061420.283427122854100
2.0074-2.0460.29371410.272626742815100
2.046-2.08780.33551410.264126822823100
2.0878-2.13320.29521420.248126812823100
2.1332-2.18280.26851400.247226732813100
2.1828-2.23740.30191410.245226822823100
2.2374-2.29790.261420.242626992841100
2.2979-2.36550.30431430.2312706284999
2.3655-2.44190.2711420.216326972839100
2.4419-2.52920.21881410.210226832824100
2.5292-2.63040.20081430.203527122855100
2.6304-2.75010.22281420.204327142856100
2.7501-2.89510.20131410.197226942835100
2.8951-3.07650.21921430.204127092852100
3.0765-3.31410.18571440.193427342878100
3.3141-3.64750.18721440.17872737288199
3.6475-4.17530.15191440.15942734287899
4.1753-5.26010.15251460.15572779292599
5.2601-68.73620.22161540.18512904305899
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)
10.80630.03960.29691.6465-0.78111.2168-0.0911-0.21240.01830.27530.06430.0074-0.364-0.42560.03250.39630.095-0.02290.4565-0.09380.300116.2612.35872.1452
21.86150.09270.48920.9708-0.09111.1587-0.0967-0.05830.0562-0.0680.0621-0.1008-0.2069-0.010.04290.23910.00180.00520.1823-0.02770.210628.99231.0513-16.8378
33.01790.1230.17672.511-0.28472.6629-0.03840.4809-0.2436-0.29260.1007-0.21670.030.1728-0.01240.2895-0.0109-0.01920.3275-0.09390.301916.9752-13.675-33.128
46.28510.3642-0.68748.7434.60675.6188-0.05351.0949-0.1675-0.7831-0.13590.0275-0.70620.35440.10490.66980.1815-0.10820.50890.09010.56883.609317.3477-35.4814
50.46250.77340.3461.6258-0.21952.1662-0.2333-0.07081.21250.13330.03750.2059-0.5754-0.03230.10420.6510.0058-0.20010.31590.07910.787712.99424.7582-30.0742
60.7201-0.8912-0.5061.35570.76330.4343-0.1979-0.1179-0.2842-0.0551-0.41550.21530.1290.09780.35880.98820.25640.3120.83120.32091.284530.065111.3262-31.2048
73.3456-1.41942.64377.45353.09984.7248-0.14090.6198-0.2627-0.2911-0.01180.3308-0.14360.19980.19330.6508-0.0696-0.00130.7318-0.02750.667440.04592.7749-28.4931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 266 through 475 )A266 - 475
2X-RAY DIFFRACTION2chain 'A' and (resid 476 through 720 )A476 - 720
3X-RAY DIFFRACTION3chain 'A' and (resid 721 through 920 )A721 - 920
4X-RAY DIFFRACTION4chain 'C' and (resid 208 through 222 )C208 - 222
5X-RAY DIFFRACTION5chain 'C' and (resid 223 through 232 )C223 - 232
6X-RAY DIFFRACTION6chain 'C' and (resid 233 through 237 )C233 - 237
7X-RAY DIFFRACTION7chain 'C' and (resid 238 through 247 )C238 - 247

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