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- PDB-6rm8: Crystal structure of the DEAH-box ATPase Prp2 in complex with Spp... -

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Basic information

Entry
Database: PDB / ID: 6rm8
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


spliceosomal complex / mRNA splicing, via spliceosome / nucleic acid binding / hydrolase activity / RNA helicase / ribonucleoprotein complex / ATP binding
Similarity search - Function
Spp2/MOS2, G-patch domain / 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 ...Spp2/MOS2, G-patch domain / 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 / 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 / RNA-binding domain superfamily / 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
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / RNA helicase / Putative pre-mRNA splicing protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 / 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.ptnr2_auth_seq_id

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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)80,39318
Polymers78,6552
Non-polymers1,73816
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-194 kcal/mol
Surface area30300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.340, 75.460, 154.440
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: 73420.078 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 , 7 types, 206 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 6.5, 350 mM calcium acetate, 19% (w/v) PEG4000

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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: 1.95→42.526 Å / Num. obs: 55604 / % possible obs: 100 % / Redundancy: 9.368 % / Biso Wilson estimate: 46.621 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.078 / Χ2: 1.041 / Net I/σ(I): 15.97 / Num. measured all: 520880 / Scaling rejects: 27
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
1.95-2.059.7531.3352.0874261761976140.811.40799.9
2.05-2.159.4950.8143.3959828630263010.9010.86100
2.15-2.258.9050.5644.7246404521552110.9410.59899.9
2.25-2.59.770.3477.9495093973397330.9790.366100
2.5-2.79.2850.20911.5150383542854260.990.221100
2.7-39.6340.11518.0654565566556640.9960.121100
3-3.59.2720.06627.0352553567056680.9980.07100
3.5-4.29.090.04338.7737549413141310.9990.045100
4.2-58.7870.03744.1220420232723240.9990.03999.9
5-68.4270.03743.6512135144114400.9990.03999.9
6-88.9020.03649.2910504118011800.9990.038100
8-107.8730.03352.0433384264240.9990.03599.5
10-208.1730.03252.8934414214210.9990.034100
20-506.250.03345.2640066640.9990.03697
50-42.526264375

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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: 1.95→42.526 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.27
RfactorNum. reflection% reflection
Rfree0.2178 2780 5 %
Rwork0.2 --
obs0.2009 55587 99.94 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 190.48 Å2 / Biso mean: 54.3042 Å2 / Biso min: 24.09 Å2
Refinement stepCycle: final / Resolution: 1.95→42.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 97 190 5741
Biso mean--79.32 50.32 -
Num. residues----700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-1.98360.34641370.322625902727
1.9836-2.01970.30541370.31826092746
2.0197-2.05850.34431350.302325682703
2.0585-2.10050.32041390.286926272766
2.1005-2.14620.29521380.258226382776
2.1462-2.19610.2721350.25725642699
2.1961-2.2510.28461380.250926152753
2.251-2.31190.25351380.225626202758
2.3119-2.37990.2351390.218726332772
2.3799-2.45670.25491360.226725932729
2.4567-2.54450.24011390.220626342773
2.5445-2.64640.23251370.229826142751
2.6464-2.76680.22221400.216226452785
2.7668-2.91270.27741400.214726652805
2.9127-3.09510.23011390.216826412780
3.0951-3.3340.26011380.219126312769
3.334-3.66930.17941410.190426682809
3.6693-4.19990.20011420.164326962838
4.1999-5.28980.16761420.153427032845
5.2898-42.53640.18181500.180628533003
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)
10.99030.15680.20031.11591.1441.316-0.15180.2669-0.0071-0.50130.07260.1555-0.54280.11520.05380.5403-0.1016-0.07990.39910.03880.2943-16.38442.8916-0.8178
21.99990.21540.81411.00210.76461.598-0.1116-0.0789-0.0536-0.1178-0.13280.2899-0.2218-0.37950.14460.32340.0234-0.05570.3192-0.01770.389-29.36790.918117.8155
31.9980.16880.16521.91210.16832.29530.0084-0.1315-0.13020.05430.11760.27340.1052-0.2976-0.0230.2715-0.0064-0.04970.29730.07960.376-17.6218-13.729434.5303
43.27270.84280.41156.4725-1.74074.59070.0409-0.3677-0.01620.3098-0.0836-0.0321-0.629-0.01990.03910.4036-0.0359-0.09260.3242-0.01860.3942-3.223816.516837.1053
54.3972-0.47870.63932.99150.33894.1186-0.314-0.23410.6533-0.270.20250.8045-0.6283-0.4730.28470.61380.0199-0.20580.3969-0.02710.8075-12.667924.098831.9438
60.0041-0.0030.00340.0022-0.00240.003-0.018-0.30110.11550.1154-0.203-0.0252-0.65290.02520.36090.81060.0133-0.11110.9429-0.17461.364-29.641511.036631.5889
73.4190.37360.85392.77512.21754.82730.0385-1.1909-0.13520.5622-0.31980.1941-0.3792-0.91150.36220.52830.0587-0.18061.0275-0.22930.8341-41.15956.658432.5139
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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