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

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Basic information

Entry
Database: PDB / ID: 6rmb
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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RNA helicase / Pre-mRNA-splicing factor
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2May 15, 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / refine / 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 / _refine.pdbx_diffrn_id / _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
D: Putative pre-mRNA splicing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5224
Polymers76,0702
Non-polymers4522
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-44 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.360, 72.640, 70.270
Angle α, β, γ (deg.)90.000, 93.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative mRNA splicing factor


Mass: 70835.133 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES/NaOH pH 7, 8% (w/v) polyvinyl alcohol, 7.5% (v/v) isopropyl alcohol

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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: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→70.154 Å / Num. obs: 23946 / % possible obs: 98.5 % / Redundancy: 3.159 % / Biso Wilson estimate: 55.348 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.094 / Χ2: 1.015 / Net I/σ(I): 12.16 / Num. measured all: 75644 / Scaling rejects: 2
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
2.5-2.63.0720.6611.928192270326670.7930.79898.7
2.6-2.73.1110.5082.576971227422410.8640.61498.5
2.7-33.2160.3284.1116462519051180.930.39498.6
3-3.53.1880.1568.5716422519251520.9820.18899.2
3.5-43.1430.0716.439076291628880.9940.08599
4-53.1010.03924.28903291628710.9970.04898.5
5-63.250.03825.954141129512740.9980.04698.4
6-83.2340.03131.333257103410070.9980.03797.4
8-103.1870.0245.4211443783590.9990.02495
10-143.0290.01849.337212502380.9990.02195.2
14-172.9140.02247.06169665810.02787.9
17-502.5690.02438.1518581720.9980.03188.9
50-70.154115120

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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 / Resolution: 2.5→70.154 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.1
RfactorNum. reflection% reflection
Rfree0.258 1197 5 %
Rwork0.2081 --
obs0.2107 23930 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 150.68 Å2 / Biso mean: 61.5954 Å2 / Biso min: 26.97 Å2
Refinement stepCycle: final / Resolution: 2.5→70.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4990 0 28 4 5022
Biso mean--63.02 47.8 -
Num. residues----656
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.60010.38051330.32432529266299
2.6001-2.71840.34521310.30262490262199
2.7184-2.86170.36311310.28392502263399
2.8617-3.0410.29261340.24992529266399
3.041-3.27580.31171330.24132525265899
3.2758-3.60550.27971330.22332535266899
3.6055-4.12710.23661340.18312546268099
4.1271-5.19950.21811340.16422535266998
5.1995-70.18170.20221340.17562542267696
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)
11.33210.12370.06081.44490.23871.6601-0.09190.03860.0639-0.1636-0.00690.5801-0.1712-0.19390.06590.3160.0083-0.08280.35720.06010.72867.862924.775428.9066
20.60410.08060.0571.51570.26861.367-0.12090.1459-0.1319-0.3140.04030.55560.0775-0.30330.0670.452-0.0681-0.19410.478-0.02330.68738.20794.087611.4692
30.8904-0.2922-0.42661.80830.04081.2933-0.07540.06440.1212-0.27350.0723-0.0503-0.00360.03940.01960.3114-0.046-0.01980.31570.02430.3936.5119.677917.7929
46.00170.5434-2.8331.1621-0.60316.5056-0.5257-0.273-0.7260.23470.1138-0.04480.03190.82810.42930.49840.0568-0.05910.4677-0.02180.530836.85413.875844.5697
51.135-0.6293-1.45970.40070.83041.8868-0.01950.3697-0.05950.34040.08530.28670.5998-0.7545-0.26170.72470.10160.07630.47460.12350.409524.9178-0.946744.8509
62.3349-0.6951-3.10170.68081.37714.6086-0.5696-0.0754-0.0952-0.00840.41960.39820.1078-0.29010.27530.6447-0.00970.00530.4998-0.00120.673917.9185-9.150515.2119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 288 through 475 )A288 - 475
2X-RAY DIFFRACTION2chain 'A' and (resid 476 through 652 )A476 - 652
3X-RAY DIFFRACTION3chain 'A' and (resid 653 through 919 )A653 - 919
4X-RAY DIFFRACTION4chain 'D' and (resid 208 through 222 )D208 - 222
5X-RAY DIFFRACTION5chain 'D' and (resid 223 through 233 )D223 - 233
6X-RAY DIFFRACTION6chain 'D' and (resid 236 through 247 )D236 - 247

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