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- PDB-6zm2: Crystal structure of the DEAH-box ATPase Prp2 in complex with ADP... -

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Basic information

Entry
Database: PDB / ID: 6zm2
TitleCrystal structure of the DEAH-box ATPase Prp2 in complex with ADP-BeF3 and ssRNA
Components
  • Putative mRNA splicing factor
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE / Prp2 / DEAH-box / spliceosome / RNA
Function / homology
Function and homology information


catalytic step 2 spliceosome / RNA splicing / helicase activity / mRNA processing / hydrolase activity / RNA helicase / RNA binding / ATP binding / metal ion binding
Similarity search - Function
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 ...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 / BERYLLIUM TRIFLUORIDE ION / HEXANE-1,6-DIOL / DI(HYDROXYETHYL)ETHER / S-1,2-PROPANEDIOL / N-PROPANOL / RNA / RNA helicase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHamann, F. / Ficner, R.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: The structure of Prp2 bound to RNA and ADP-BeF 3 - reveals structural features important for RNA unwinding by DEAH-box ATPases.
Authors: Hamann, F. / Zimmerningkat, L.C. / Becker, R.A. / Garbers, T.B. / Neumann, P. / Hub, J.S. / Ficner, R.
History
DepositionJul 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,72530
Polymers73,1012
Non-polymers2,62428
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint38 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.660, 100.410, 140.950
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 / RNA chain , 2 types, 2 molecules AB

#1: Protein Putative mRNA splicing factor


Mass: 70696.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063660 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SEG4
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 2404.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 12 types, 225 molecules

#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#11: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#12: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O
#13: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM MOPS Na-HEPES, 8% PEG20000, 22% PEGMME 550, 20mM 1,6-hexanediol, 20mM 1-butanol, 20mM 1,2-propanediol, 20mM 2-propanol, 20mM 1,4-butandiol, 20mM 1,3-propanediol

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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: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→81.78 Å / Num. obs: 41019 / % possible obs: 99.5 % / Redundancy: 13.677 % / Biso Wilson estimate: 42.296 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.131 / Χ2: 0.974 / Net I/σ(I): 14.88 / Num. measured all: 561018 / Scaling rejects: 28
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
2.1-2.213.9011.2792.2172672528052280.8131.32699
2.2-2.314.0210.9273.1161201439543650.8970.96199.3
2.3-2.4513.9490.6724.2974207535253200.9360.69799.4
2.45-2.613.7430.4735.9857267418341670.9630.49199.6
2.6-2.813.6740.338.258677430642910.9820.34399.7
2.8-313.5440.22911.2743680323932250.9910.23899.6
3-413.6020.09522.87111390820481890.9990.09999.8
4-513.3720.05240.9639729297129710.9990.054100
5-613.0370.05538.7217365134013320.9990.05799.4
6-1013.2910.03851.34197501486148610.04100
10-2011.8050.02867.26454538638510.02999.7
20-509.2810.02959.35529625710.0391.9
50-81.7823.7060.9164315.24275

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6fac

6fac


Resolution: 2.1→81.78 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 2048 5 %
Rwork0.1852 38952 -
obs0.1875 41000 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.1 Å2 / Biso mean: 45.9937 Å2 / Biso min: 21.57 Å2
Refinement stepCycle: final / Resolution: 2.1→81.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 136 168 200 5344
Biso mean--63.42 48.57 -
Num. residues----635
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.2791330.2572524265799
2.15-2.20.27961330.24612535266899
2.2-2.260.25861330.23342545267899
2.26-2.330.27451370.22112595273299
2.33-2.40.27041330.20892536266999
2.4-2.490.2661350.211225602695100
2.49-2.590.22891350.20322566270199
2.59-2.710.23321370.189926032740100
2.71-2.850.21431360.18825812717100
2.85-3.030.20751360.18052587272399
3.03-3.260.25791380.184226072745100
3.26-3.590.20611360.177125992735100
3.59-4.110.20791400.158426452785100
4.11-5.180.20661400.155326662806100
5.18-81.780.27371460.19682803294999
Refinement TLS params.Method: refined / Origin x: 5.3273 Å / Origin y: 11.5924 Å / Origin z: -32.1584 Å
111213212223313233
T0.2415 Å20.0144 Å2-0.0145 Å2-0.2133 Å2-0.0201 Å2--0.2602 Å2
L0.5962 °2-0.0484 °20.2655 °2-0.5232 °2-0.5684 °2--1.2573 °2
S-0.0115 Å °-0.0322 Å °0.0718 Å °0.0422 Å °-0.0282 Å °-0.0448 Å °-0.0603 Å °0.0539 Å °0.0431 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA289 - 918
2X-RAY DIFFRACTION1allA1101
3X-RAY DIFFRACTION1allB2 - 9
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF2 - 223
7X-RAY DIFFRACTION1allG2 - 6
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allI1 - 2
10X-RAY DIFFRACTION1allJ2
11X-RAY DIFFRACTION1allK1001 - 1701
12X-RAY DIFFRACTION1allL1101
13X-RAY DIFFRACTION1allM1301 - 2005
14X-RAY DIFFRACTION1allN1801 - 2202

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