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- PDB-4qu4: Improved refinement of the Mtr4 apo crystal structure -

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Basic information

Entry
Database: PDB / ID: 4qu4
TitleImproved refinement of the Mtr4 apo crystal structure
ComponentsATP-dependent RNA helicase DOB1
KeywordsHYDROLASE / rec-A FOLD / winged-helix-turn-helix / antiparallel-coiled-coil / DSHCT domain / helicase / nucleotide binding / phosphoprotein / rRNA processing / TRAMP / ATP binding / nucleus
Function / homology
Function and homology information


TRAMP complex / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / U5 snRNA 3'-end processing / RNA fragment catabolic process / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...TRAMP complex / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / U5 snRNA 3'-end processing / RNA fragment catabolic process / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA catabolic process / 3'-5' RNA helicase activity / nuclear mRNA surveillance / poly(A) binding / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA processing / RNA helicase activity / oxidoreductase activity / RNA helicase / mRNA binding / nucleolus / ATP hydrolysis activity / DNA binding / ATP binding / nucleus
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #300 / YheA-like fold - #20 / YheA-like fold / Sec63 N-terminal domain-like fold - #30 / Sec63 N-terminal domain-like fold / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : ...Elongation Factor Tu (Ef-tu); domain 3 - #300 / YheA-like fold - #20 / YheA-like fold / Sec63 N-terminal domain-like fold - #30 / Sec63 N-terminal domain-like fold / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / Prismane-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / 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 / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / ATP-dependent RNA helicase DOB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.392 Å
AuthorsJohnson, S.J. / Taylor, L.L.
Citation
Journal: Nucleic Acids Res. / Year: 2014
Title: The Mtr4 ratchet helix and arch domain both function to promote RNA unwinding.
Authors: Taylor, L.L. / Jackson, R.N. / Rexhepaj, M. / King, A.K. / Lott, L.K. / van Hoof, A. / Johnson, S.J.
#1: Journal: Embo J. / Year: 2010
Title: The crystal structure of MTR4 reveals a novel arch domain required for rRNA processing.
Authors: Jackson, R.N. / Klauer, A.A. / Hintze, B.J. / Robinson, H. / van Hoof, A. / Johnson, S.J.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionDec 3, 2014ID: 3L9O
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase DOB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5794
Polymers126,2941
Non-polymers2853
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.516, 133.516, 190.949
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ATP-dependent RNA helicase DOB1 / mRNA transport regulator MTR4


Mass: 126294.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DOB1, J1158, MTR4, MTR4/YJL050W, YJL050W / Plasmid: pET151 Directional TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P47047, RNA helicase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4

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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: 3.89 Å3/Da / Density % sol: 68.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.4 M ammonium dihydrogen phosphate, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 19, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.389→30 Å / Num. all: 26177 / Num. obs: 26177 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 137.4 Å2
Reflection shellResolution: 3.389→3.52 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.494 / % possible all: 59.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.392→28.757 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 38.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2991 1268 4.86 %
Rwork0.2475 --
obs0.2502 26095 93.82 %
all-26095 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 164.45 Å2
Refinement stepCycle: LAST / Resolution: 3.392→28.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6665 0 15 0 6680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016789
X-RAY DIFFRACTIONf_angle_d1.4639265
X-RAY DIFFRACTIONf_dihedral_angle_d14.9522290
X-RAY DIFFRACTIONf_chiral_restr0.0521123
X-RAY DIFFRACTIONf_plane_restr0.0071196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.392-3.52780.3918960.35391746X-RAY DIFFRACTION60
3.5278-3.68810.42551230.34232464X-RAY DIFFRACTION85
3.6881-3.88210.38331540.32062881X-RAY DIFFRACTION99
3.8821-4.12460.31671370.2932888X-RAY DIFFRACTION100
4.1246-4.4420.30431380.24852943X-RAY DIFFRACTION100
4.442-4.88710.29871490.22192913X-RAY DIFFRACTION100
4.8871-5.58980.33051430.25192951X-RAY DIFFRACTION100
5.5898-7.02550.33681550.31242973X-RAY DIFFRACTION100
7.0255-28.75830.24991730.19833068X-RAY DIFFRACTION100
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)
11.4901-1.06261.51180.7245-1.03921.477-0.4911-0.53640.54640.83970.5707-1.08940.88780.6098-01.4882-0.57180.26471.6363-0.37161.8414121.405354.191481.9824
23.94612.79573.18364.4006-0.7886.6049-0.0764-0.49190.77720.0887-0.41640.34070.277-0.3368-0.00010.8181-0.13930.26571.1179-0.30271.4826117.508651.830255.8376
32.66380.7969-1.44615.41081.61213.2597-0.0921-0.73130.6103-0.66950.8091-0.7377-0.28630.6662-01.5352-0.35860.10141.5788-0.31721.3137101.934964.183787.3387
42.22770.1277-0.08080.74230.1021.49460.1456-0.19490.3534-1.9922-0.59730.0948-2.5728-0.9086-0.14194.98420.0373-0.22471.015-0.01511.66595.373279.665666.3684
51.09020.25291.23923.39274.62786.2213-0.63960.29960.2742-1.52290.6201-0.0506-1.43090.378-0.00041.8011-0.4140.16731.5463-0.18931.4673100.15655.545271.3988
61.04271.7733-0.83132.6099-1.55781.779-0.3803-0.8651-0.5577-0.52510.003-0.73330.19240.9719-01.59430.04250.2551.79750.06881.546390.496622.556770.4676
75.52181.64661.8743.07450.67173.89790.3039-0.5016-0.10940.37160.01910.06220.490.4328-01.38070.35540.02931.5862-0.07461.436471.454344.533182.5487
81.4806-1.1511-0.77193.55860.15842.1061-0.0988-0.53610.0787-0.15490.02810.3412-0.25930.322801.6927-0.00180.07561.51410.17651.534572.657725.587583.1105
90.8322-0.75010.20442.2311-0.2693-0.0238-0.58770.16230.0311-1.64560.1161.1313-0.749-0.6646-0.00012.3586-0.1513-0.21262.3193-0.05161.879982.71746.199843.0707
101.0882-0.1273-0.52640.03940.21210.5071-0.4152-0.20020.69480.279-0.67910.0441-1.0321-0.923-0.0183.54750.3674-0.20592.53580.21041.53585.907567.173145.1656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 79:122)
2X-RAY DIFFRACTION2(chain A and resid 123:321)
3X-RAY DIFFRACTION3(chain A and resid 322:415)
4X-RAY DIFFRACTION4(chain A and resid 416:496)
5X-RAY DIFFRACTION5(chain A and resid 497:599)
6X-RAY DIFFRACTION6(chain A and resid 600:661)
7X-RAY DIFFRACTION7(chain A and resid 662:780)
8X-RAY DIFFRACTION8(chain A and resid 781:877)
9X-RAY DIFFRACTION9(chain A and resid 878:995)
10X-RAY DIFFRACTION10(chain A and resid 996:1072)

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