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

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Basic information

Entry
Database: PDB / ID: 6rmc
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 / helicase activity / mRNA processing / hydrolase activity / RNA helicase / RNA binding / ATP binding / nucleus / metal ion 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 / RNA helicase / Putative pre-mRNA splicing protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsHamann, F. / Neumann, P. / Schmitt, A. / 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: Data collection / Database references ...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 / 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.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: Putative mRNA splicing factor
B: Putative mRNA splicing factor
C: Putative pre-mRNA splicing protein
D: Putative pre-mRNA splicing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,2148
Polymers156,3114
Non-polymers9034
Water2,090116
1
A: Putative mRNA splicing factor
C: Putative pre-mRNA splicing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6074
Polymers78,1562
Non-polymers4522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-44 kcal/mol
Surface area29460 Å2
MethodPISA
2
B: Putative mRNA splicing factor
D: Putative pre-mRNA splicing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6074
Polymers78,1562
Non-polymers4522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-43 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.730, 113.690, 191.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (NAME CA OR NAME N OR NAME...
21(CHAIN B AND (NAME CA OR NAME N OR NAME...
12(CHAIN A AND (NOT (NAME CA OR NAME N OR...
22(CHAIN B AND (NOT (NAME CA OR NAME N OR...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN A AND (NAME CA OR NAME N OR NAME...A278 - 919
121(CHAIN A AND (NAME CA OR NAME N OR NAME...A278 - 919
131(CHAIN A AND (NAME CA OR NAME N OR NAME...A278 - 919
141(CHAIN A AND (NAME CA OR NAME N OR NAME...A278 - 919
211(CHAIN B AND (NAME CA OR NAME N OR NAME...B270 - 920
221(CHAIN B AND (NAME CA OR NAME N OR NAME...B270 - 920
231(CHAIN B AND (NAME CA OR NAME N OR NAME...B270 - 920
241(CHAIN B AND (NAME CA OR NAME N OR NAME...B270 - 920
112(CHAIN A AND (NOT (NAME CA OR NAME N OR...A0
212(CHAIN B AND (NOT (NAME CA OR NAME N OR...B270 - 920
222(CHAIN B AND (NOT (NAME CA OR NAME N OR...B270 - 920
232(CHAIN B AND (NOT (NAME CA OR NAME N OR...B270 - 920
242(CHAIN B AND (NOT (NAME CA OR NAME N OR...B270 - 920

NCS ensembles :
ID
1
2

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Components

#1: Protein Putative mRNA splicing factor


Mass: 72920.586 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 270-921
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.: 2 / Fragment: UNP RESIDUES 211-254
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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bicine/Trizma pH 7.5, 11% (w/v) PEG8000, 20% (w/v) ethylene glycol, 20 mM of a monosaccharide mixture (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose and N-acetyl-D-glucosamine)

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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 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 50939 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.04 % / Biso Wilson estimate: 62.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.077 / Χ2: 0.963 / Net I/σ(I): 17.33 / Num. measured all: 256605
Reflection shellResolution: 2.6→2.71 Å / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 6069 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YB2

4yb2
PDB Unreleased entry


Resolution: 2.6→48.896 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.57
RfactorNum. reflection% reflection
Rfree0.2504 2547 5.01 %
Rwork0.2222 --
obs0.2235 50847 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 160.73 Å2 / Biso mean: 69.5289 Å2 / Biso min: 32.44 Å2
Refinement stepCycle: final / Resolution: 2.6→48.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10755 0 56 116 10927
Biso mean--80.12 45.08 -
Num. residues----1375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411037
X-RAY DIFFRACTIONf_angle_d0.53914978
X-RAY DIFFRACTIONf_chiral_restr0.041704
X-RAY DIFFRACTIONf_plane_restr0.0041933
X-RAY DIFFRACTIONf_dihedral_angle_d16.1026740
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1845X-RAY DIFFRACTIONPOSITIONAL0.298
12B1845X-RAY DIFFRACTIONPOSITIONAL0.298
21A2380X-RAY DIFFRACTIONPOSITIONAL0.307
22B2380X-RAY DIFFRACTIONPOSITIONAL0.307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6001-2.65010.4081390.380826322771100
2.6501-2.70420.39711420.366826772819100
2.7042-2.7630.36981400.344826422782100
2.763-2.82730.32281380.30392639277799
2.8273-2.8980.36591400.294526652805100
2.898-2.97630.3291400.290726452785100
2.9763-3.06390.31591380.28926352773100
3.0639-3.16270.3221420.284426872829100
3.1627-3.27580.29831390.268926452784100
3.2758-3.40690.30561410.260826682809100
3.4069-3.56190.29211410.242726852826100
3.5619-3.74960.24771410.225426692810100
3.7496-3.98440.20791420.203727022844100
3.9844-4.29190.21991410.191326742815100
4.2919-4.72350.22791430.17582721286499
4.7235-5.40630.18431440.179827292873100
5.4063-6.80840.26961450.216327502895100
6.8084-48.90450.18781510.17612835298698
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)
11.90160.13191.05530.76060.1731.1987-0.01620.51020.3061-0.2132-0.108-0.0670.02120.2089-0.05170.49110.06010.00610.54590.13380.47869.33719.9249-50.8535
22.30171.56650.65493.88070.77371.75-0.10690.0507-0.3993-0.23660.1957-0.03770.20840.12820.00020.42280.0449-0.07230.41190.00060.562917.4168-15.1258-35.8279
31.5752-0.0938-0.24591.3448-1.07783.35070.12-0.25970.0730.2461-0.06440.0337-0.44260.2297-0.00320.5578-0.0740.07580.4446-0.08390.4027-18.325216.613813.8251
41.60.0303-1.11350.60030.79711.8414-0.2238-0.50440.11810.37790.3259-0.69740.12151.12350.03760.63290.119-0.13081.0266-0.10240.50353.85646.0283.9219
51.5413-0.589-0.30981.02630.72630.3288-0.1109-0.3026-0.09670.32890.3148-0.06120.36440.50020.04970.62590.107-0.06760.838-0.02650.3772-1.08532.40254.3748
60.657-0.0001-0.22420.86430.50041.6585-0.02550.08750.08420.04560.05940.0499-0.24890.0930.07340.52960.0113-0.05370.5979-0.01510.4537-16.0679.7476-11.2772
72.2371-1.08410.38854.00270.62713.2778-0.17140.1744-0.53910.6215-0.0239-0.0660.74140.1968-0.05230.60150.01470.0070.3925-0.02530.5634-21.1757-15.7665-8.9352
80.3132-0.2173-0.11790.74390.29350.11710.4163-0.7742-1.26251.0464-0.3271-0.26070.5088-0.0158-0.00290.6349-0.0096-0.20620.6523-0.04110.829528.65133.9054-17.2596
90.1377-0.147-0.00340.10980.01670.0220.0605-0.08330.47050.02620.14550.1983-0.1218-0.09550.00010.7390.01470.03790.8619-0.1760.865517.597610.8821-19.0394
101.4596-0.13320.7810.1210.42482.29270.8527-0.1565-0.49530.4944-0.56170.26030.9214-0.50580.13220.53330.05450.01030.7571-0.080.6009-4.07891.7347-28.203
110.06680.0477-0.09860.0396-0.0580.1128-0.91920.23-0.45150.4066-0.34890.03380.45670.0332-0.0020.6252-0.01050.03430.49750.0470.6686-6.5426-7.1622-32.9964
120.20550.1068-0.19850.0773-0.02520.1849-0.38981.3924-0.5901-1.370.18730.35220.41730.2939-0.00010.7821-0.0076-0.00051.34060.07550.8902-26.753410.7797-28.0893
130.05210.09760.11740.17880.23660.2656-0.37880.11390.74790.540.248-0.3752-0.63480.449-0.00010.67480.12620.0851.12990.22080.7913-17.200617.0481-25.391
140.07820.0787-0.05060.0714-0.07850.22940.24760.24820.3349-0.1744-0.1637-0.29840.14350.24330.00030.55370.0763-0.06550.7851-0.02060.5241.84060.9141-16.8992
150.0661-0.01-0.03150.02110.04760.1097-0.78640.0457-1.1264-0.0960.30620.39620.578-0.0543-0.00420.5848-0.01790.08240.85820.11190.75653.3414-8.4763-11.9829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 278 through 669 )A278 - 669
2X-RAY DIFFRACTION2chain 'A' and (resid 670 through 919 )A670 - 919
3X-RAY DIFFRACTION3chain 'B' and (resid 270 through 450 )B270 - 450
4X-RAY DIFFRACTION4chain 'B' and (resid 451 through 532 )B451 - 532
5X-RAY DIFFRACTION5chain 'B' and (resid 533 through 627 )B533 - 627
6X-RAY DIFFRACTION6chain 'B' and (resid 628 through 721 )B628 - 721
7X-RAY DIFFRACTION7chain 'B' and (resid 722 through 920 )B722 - 920
8X-RAY DIFFRACTION8chain 'C' and (resid 211 through 222 )C211 - 222
9X-RAY DIFFRACTION9chain 'C' and (resid 223 through 234 )C223 - 234
10X-RAY DIFFRACTION10chain 'C' and (resid 235 through 248 )C235 - 248
11X-RAY DIFFRACTION11chain 'C' and (resid 249 through 254 )C249 - 254
12X-RAY DIFFRACTION12chain 'D' and (resid 211 through 221 )D211 - 221
13X-RAY DIFFRACTION13chain 'D' and (resid 222 through 233 )D222 - 233
14X-RAY DIFFRACTION14chain 'D' and (resid 234 through 248 )D234 - 248
15X-RAY DIFFRACTION15chain 'D' and (resid 249 through 254 )D249 - 254

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