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- PDB-5ltj: Crystal structure of the Prp43-ADP-BeF3 complex (in orthorhombic ... -

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Basic information

Entry
Database: PDB / ID: 5ltj
TitleCrystal structure of the Prp43-ADP-BeF3 complex (in orthorhombic space group)
ComponentsPre-mRNA-splicing factor ATP-dependent RNA helicase PRP43
KeywordsHYDROLASE / Spliceosome / RNA HELICASE / DEAH-BOX PROTEIN / DHX15
Function / homology
Function and homology information


RNA splicing / spliceosomal complex / mRNA processing / RNA helicase activity / hydrolase activity / RNA helicase / RNA binding / ATP binding / metal ion 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 (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. ...DHX15, DEXH-box helicase 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 / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / RNA helicase
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsTauchert, M.J. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
CitationJournal: Elife / Year: 2017
Title: Structural insights into the mechanism of the DEAH-box RNA helicase Prp43.
Authors: Tauchert, M.J. / Fourmann, J.B. / Luhrmann, R. / Ficner, R.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 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_label_atom_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,34217
Polymers81,6411
Non-polymers1,70116
Water12,394688
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-134 kcal/mol
Surface area31510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.826, 105.637, 119.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 81641.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS EXPRESSED WITH 2 ADDITIONAL N-TERMINAL AMINO ACIDS (MA) AND A C-TERMINAL STREP-TAG (WSHPQFEK).
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0005780 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0RY84

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Non-polymers , 8 types, 704 molecules

#2: 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
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 35 % (v/v) MPD, 1.67 % (w/v) PEG 4000 and 100 mM Na HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.78→79.02 Å / Num. obs: 107277 / % possible obs: 99.6 % / Redundancy: 4.71 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.88
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 4.66 % / Rmerge(I) obs: 1.235 / Mean I/σ(I) obs: 1.64 / CC1/2: 0.619 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LTA

5lta


Resolution: 1.78→67.986 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.87
RfactorNum. reflection% reflection
Rfree0.1989 1957 1.82 %
Rwork0.1766 --
obs0.177 107254 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→67.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5638 0 105 688 6431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045951
X-RAY DIFFRACTIONf_angle_d0.878082
X-RAY DIFFRACTIONf_dihedral_angle_d13.7272276
X-RAY DIFFRACTIONf_chiral_restr0.032899
X-RAY DIFFRACTIONf_plane_restr0.0041035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7801-1.82460.40881380.35477266X-RAY DIFFRACTION98
1.8246-1.87390.32181400.31857447X-RAY DIFFRACTION100
1.8739-1.92910.32141390.28857479X-RAY DIFFRACTION100
1.9291-1.99130.28731400.25697483X-RAY DIFFRACTION100
1.9913-2.06250.2421340.2337444X-RAY DIFFRACTION100
2.0625-2.14510.22591390.20937477X-RAY DIFFRACTION100
2.1451-2.24270.27471400.19397492X-RAY DIFFRACTION100
2.2427-2.3610.1811400.18767475X-RAY DIFFRACTION100
2.361-2.50890.21821400.18337496X-RAY DIFFRACTION100
2.5089-2.70260.2091390.17687581X-RAY DIFFRACTION100
2.7026-2.97460.20281400.17317542X-RAY DIFFRACTION100
2.9746-3.4050.18681380.16277599X-RAY DIFFRACTION100
3.405-4.28990.16851430.13467620X-RAY DIFFRACTION100
4.2899-68.03530.14861470.1487896X-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)
11.04450.22350.31322.12260.95561.6183-0.0267-0.025-0.04990.10920.1607-0.20310.09910.3749-0.09230.11950.038100.2481-0.05070.125311.7562208.168423.3128
21.51950.88811.43891.22351.21492.6145-0.0417-0.11130.1487-0.0466-0.14760.2944-0.0837-0.39790.11280.11330.0478-0.01910.2211-0.06940.1899-13.811218.917428.2648
30.8763-0.05860.7180.432-0.43693.8206-0.04530.1999-0.0373-0.14270.0314-0.0663-0.13180.4973-0.01160.1999-0.0234-0.00510.2472-0.06450.207217.0908223.963249.2582
42.1560.0099-0.16681.29190.32372.2451-0.0508-0.052-0.4369-0.00960.01840.17810.189-0.34380.0160.1316-0.0462-0.00580.1170.01320.1798-7.1896221.531262.701
52.6538-0.26740.60291.74130.3242.55690-0.26840.16940.05060.0721-0.1332-0.27220.1168-0.04980.1818-0.0097-0.00030.1665-0.03350.15756.4476235.095869.9814
63.7013-0.4880.52835.4915-2.14147.6417-0.2024-0.8278-0.39731.42250.297-0.25960.38830.6422-0.1340.51870.0457-0.12110.4524-0.20330.336619.2599235.641185.1153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 60:275
2X-RAY DIFFRACTION2chain A and resseq 276:460
3X-RAY DIFFRACTION3chain A and resseq 461:527
4X-RAY DIFFRACTION4chain A and resseq 528:640
5X-RAY DIFFRACTION5chain A and resseq 641:741
6X-RAY DIFFRACTION6chain A and resseq 742:762

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