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- PDB-5suq: Crystal structure of the THO-Sub2 complex -

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Basic information

Entry
Database: PDB / ID: 5suq
TitleCrystal structure of the THO-Sub2 complex
Components
  • ATP-dependent RNA helicase SUB2
  • Tex1
  • Tho2, Hpr1, Mft1, and Thp2
KeywordsHYDROLASE / mRNA export
Function / homology
Function and homology information


transcription export complex / mRNA 3'-end processing / mRNA export from nucleus / subtelomeric heterochromatin formation / transcription-coupled nucleotide-excision repair / spliceosomal complex / transcription elongation by RNA polymerase II / mRNA splicing, via spliceosome / chromosome, telomeric region / RNA helicase activity ...transcription export complex / mRNA 3'-end processing / mRNA export from nucleus / subtelomeric heterochromatin formation / transcription-coupled nucleotide-excision repair / spliceosomal complex / transcription elongation by RNA polymerase II / mRNA splicing, via spliceosome / chromosome, telomeric region / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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 ...RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
12-TUNGSTOPHOSPHATE / ATP-dependent RNA helicase SUB2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 6 Å
AuthorsRen, Y. / Blobel, G.
CitationJournal: Elife / Year: 2017
Title: Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1.
Authors: Ren, Y. / Schmiege, P. / Blobel, G.
History
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 4, 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

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Assembly

Deposited unit
A: ATP-dependent RNA helicase SUB2
B: Tex1
C: ATP-dependent RNA helicase SUB2
D: Tex1
M: Tho2, Hpr1, Mft1, and Thp2
N: Tho2, Hpr1, Mft1, and Thp2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)592,04417
Polymers560,3976
Non-polymers31,64711
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-41 kcal/mol
Surface area353240 Å2
Unit cell
Length a, b, c (Å)153.339, 319.534, 176.444
Angle α, β, γ (deg.)90.00, 100.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP-dependent RNA helicase SUB2 / Suppressor of BRR1 protein 2


Mass: 50375.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SUB2, YDL084W / Production host: Escherichia coli (E. coli) / References: UniProt: Q07478, RNA helicase
#2: Protein Tex1


Mass: 34059.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Trichoplusia ni (cabbage looper)
#3: Protein Tho2, Hpr1, Mft1, and Thp2


Mass: 195762.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Trichoplusia ni (cabbage looper)
#4: Chemical
ChemComp-KEG / 12-TUNGSTOPHOSPHATE


Mass: 2877.030 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: O40PW12
Compound detailsTHE DEPOSITORS STATE THAT BECAUSE OF THE 6.0 A RESOLUTION OF THE DATA AND LACK OF STRUCTURAL ...THE DEPOSITORS STATE THAT BECAUSE OF THE 6.0 A RESOLUTION OF THE DATA AND LACK OF STRUCTURAL MODELS, RESIDUES OF CHAIN B, D, M, AND N COULD NOT BE ASSIGNED AND ALL RESIDUES ARE UNK (UNKNOWN RESIDUES) AND RESIDUE NUMBERING IS ARBITRARY. THE DEPOSITORS STATE THAT BECAUSE OF THE LOW RESOLUTION, THE RESIDUES OF CHAIN M AND CHAIN N CAN NOT BE ASSIGNED TO INDIVIDUAL PROTEINS (THO2, HPR1, MFT1, AND THP2)
Sequence detailsCHAINS B AND D ARE TWO MOLECULES OF TEX1 PROTEIN FROM SACCHAROMYCES BAYANUS. CHAINS M AND N EACH ...CHAINS B AND D ARE TWO MOLECULES OF TEX1 PROTEIN FROM SACCHAROMYCES BAYANUS. CHAINS M AND N EACH CONTAINS FOUR SACCHAROMYCES CEREVISIAE PROTEINS, INCLUDING THO2 (UNP P53552), HPR1 (UNP P17629), MFT1 (UNP P33441), AND THP2 (UNP O13539).

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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

Crystal growTemperature: 289 K / Method: evaporation / pH: 8.4
Details: 100 mM Tris-HCl (pH 8.4), 17.5% PEG3350, 2% methanol, 0.3 M NDSB-195

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2123 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2123 Å / Relative weight: 1
ReflectionResolution: 6→50 Å / Num. obs: 41038 / % possible obs: 98.8 % / Redundancy: 6.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementStarting model: 5SUP

5sup


Resolution: 6→49.57 Å / SU ML: 1.53 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 53.87
RfactorNum. reflection% reflection
Rfree0.434 2078 5.06 %
Rwork0.436 --
obs0.436 41038 98.5 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å
Refinement stepCycle: LAST / Resolution: 6→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30205 0 583 0 30788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0130837
X-RAY DIFFRACTIONf_angle_d1.40841191
X-RAY DIFFRACTIONf_dihedral_angle_d12.5486871
X-RAY DIFFRACTIONf_chiral_restr0.0825771
X-RAY DIFFRACTIONf_plane_restr0.0045601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6-6.13930.52171310.51332474X-RAY DIFFRACTION93
6.1393-6.29260.46121380.50782578X-RAY DIFFRACTION98
6.2926-6.46240.48541380.51892590X-RAY DIFFRACTION99
6.4624-6.65210.4711400.50692609X-RAY DIFFRACTION99
6.6521-6.86630.48911360.50162555X-RAY DIFFRACTION98
6.8663-7.1110.44481390.50832625X-RAY DIFFRACTION100
7.111-7.39480.55361400.49932617X-RAY DIFFRACTION100
7.3948-7.73020.49041410.50452634X-RAY DIFFRACTION99
7.7302-8.13610.44441390.472615X-RAY DIFFRACTION99
8.1361-8.64330.40751370.42832564X-RAY DIFFRACTION98
8.6433-9.30660.39941410.39942649X-RAY DIFFRACTION100
9.3066-10.23570.36961400.38542618X-RAY DIFFRACTION100
10.2357-11.69990.34781390.36262573X-RAY DIFFRACTION97
11.6999-14.67690.41241390.38972625X-RAY DIFFRACTION99
14.6769-49.57530.51551400.47252634X-RAY DIFFRACTION98

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