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- PDB-4u4c: The molecular architecture of the TRAMP complex reveals the organ... -

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Basic information

Entry
Database: PDB / ID: 4u4c
TitleThe molecular architecture of the TRAMP complex reveals the organization and interplay of its two catalytic activities
Components
  • ATP-dependent RNA helicase DOB1
  • Protein AIR2,Poly(A) RNA polymerase protein 2
KeywordsHYDROLASE / helicase / ATPase / poly(A)polymerase / RNA degradation / exosome
Function / homology
Function and homology information


polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / meiotic DNA double-strand break formation / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing ...polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / meiotic DNA double-strand break formation / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / RNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / 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) / 3'-5' RNA helicase activity / rRNA catabolic process / polynucleotide adenylyltransferase / histone mRNA catabolic process / poly(A) RNA polymerase activity / nuclear mRNA surveillance / negative regulation of DNA recombination / poly(A) binding / tRNA modification / RNA catabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / 5'-deoxyribose-5-phosphate lyase activity / localization / base-excision repair / mRNA processing / protein-macromolecule adaptor activity / RNA helicase activity / molecular adaptor activity / oxidoreductase activity / RNA helicase / cell division / mRNA binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Poly(A) polymerase complex subunit Air1/2, budding yeast / Nucleotidyltransferase Trf4-like / : / AIR2-like, CCHC-type 1 zinc finger 4 / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / PAP/25A-associated / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal ...Poly(A) polymerase complex subunit Air1/2, budding yeast / Nucleotidyltransferase Trf4-like / : / AIR2-like, CCHC-type 1 zinc finger 4 / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / PAP/25A-associated / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / Cid1 family poly A polymerase / Prismane-like superfamily / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Nucleotidyltransferase superfamily / Helicase conserved C-terminal domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / ATP-dependent RNA helicase DOB1 / Poly(A) RNA polymerase protein 2 / Protein AIR2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFalk, S. / Weir, J.R. / Hentschel, J. / Reichelt, P. / Bonneau, F. / Conti, E.
CitationJournal: Mol.Cell / Year: 2014
Title: The Molecular Architecture of the TRAMP Complex Reveals the Organization and Interplay of Its Two Catalytic Activities.
Authors: Falk, S. / Weir, J.R. / Hentschel, J. / Reichelt, P. / Bonneau, F. / Conti, E.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: 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
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: ATP-dependent RNA helicase DOB1
B: Protein AIR2,Poly(A) RNA polymerase protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,77316
Polymers126,4112
Non-polymers1,36214
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-105 kcal/mol
Surface area45290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.184, 166.768, 131.259
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 113579.922 Da / Num. of mol.: 1 / Fragment: UNP residues 81-1073
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MTR4, DOB1, YJL050W, J1158 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: P47047, RNA helicase
#2: Protein Protein AIR2,Poly(A) RNA polymerase protein 2 / Arginine methyltransferase-interacting RING finger protein 2 / DNA polymerase kappa / DNA ...Arginine methyltransferase-interacting RING finger protein 2 / DNA polymerase kappa / DNA polymerase sigma / Topoisomerase 1-related protein TRF4


Mass: 12830.835 Da / Num. of mol.: 1
Fragment: UNP residues 1-62,UNP residues 111-160,UNP residues 1-62,UNP residues 111-160
Source method: isolated from a genetically manipulated source
Details: Fusion of Air2 residues 1-62 to Trf4 residues 111-160
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: AIR2, YDL175C, PAP2, TRF4, YOL115W, HRC584, O0716 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS
References: UniProt: Q12476, UniProt: P53632, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Non-polymers , 6 types, 235 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 0.1 M Tris pH 8.2, 0.15 M Li2SO4, 32% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→86 Å / Num. obs: 67064 / % possible obs: 99.61 % / Redundancy: 5.6 % / Net I/σ(I): 15.6
Reflection shellResolution: 2.397→2.483 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.075 / Mean I/σ(I) obs: 1.16 / % possible all: 96.52

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XGJ

2xgj


Resolution: 2.4→49.696 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.05 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 6406 4.98 %Random selection
Rwork0.2037 ---
obs0.2055 67064 98.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→49.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7724 0 78 221 8023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097942
X-RAY DIFFRACTIONf_angle_d1.12210728
X-RAY DIFFRACTIONf_dihedral_angle_d15.1542982
X-RAY DIFFRACTIONf_chiral_restr0.0451205
X-RAY DIFFRACTIONf_plane_restr0.0051376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.397-2.420.4061890.36723492X-RAY DIFFRACTION84
2.4242-2.45270.36652130.33854012X-RAY DIFFRACTION98
2.4527-2.48260.34682140.32244123X-RAY DIFFRACTION99
2.4826-2.51410.34192160.30584031X-RAY DIFFRACTION99
2.5141-2.54720.36462170.3124130X-RAY DIFFRACTION100
2.5472-2.5820.39882150.31174107X-RAY DIFFRACTION100
2.582-2.61890.38012140.31784064X-RAY DIFFRACTION100
2.6189-2.6580.32792120.30654147X-RAY DIFFRACTION100
2.658-2.69960.30412140.29254061X-RAY DIFFRACTION100
2.6996-2.74380.39752110.28964111X-RAY DIFFRACTION100
2.7438-2.79110.36132200.27754151X-RAY DIFFRACTION100
2.7911-2.84190.31832100.2834039X-RAY DIFFRACTION99
2.8419-2.89650.31882150.26954115X-RAY DIFFRACTION100
2.8965-2.95560.27912190.26644113X-RAY DIFFRACTION100
2.9556-3.01990.30492150.25894087X-RAY DIFFRACTION99
3.0199-3.09010.29482140.26964110X-RAY DIFFRACTION100
3.0901-3.16740.28762140.2584108X-RAY DIFFRACTION100
3.1674-3.2530.31482170.25024087X-RAY DIFFRACTION100
3.253-3.34870.30032070.23124121X-RAY DIFFRACTION99
3.3487-3.45680.28622140.2334083X-RAY DIFFRACTION99
3.4568-3.58030.26342120.20784091X-RAY DIFFRACTION100
3.5803-3.72360.22252070.21374099X-RAY DIFFRACTION99
3.7236-3.8930.28482180.19224090X-RAY DIFFRACTION100
3.893-4.09820.20292210.17094107X-RAY DIFFRACTION100
4.0982-4.35480.19682160.15984107X-RAY DIFFRACTION100
4.3548-4.69080.18752090.15034104X-RAY DIFFRACTION99
4.6908-5.16240.19122170.16264075X-RAY DIFFRACTION99
5.1624-5.90840.21332170.18174093X-RAY DIFFRACTION100
5.9084-7.43990.20482060.1754091X-RAY DIFFRACTION99
7.4399-49.70670.14162230.13864088X-RAY DIFFRACTION99

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