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- PDB-5sup: Crystal structure of the Sub2-Yra1 complex in association with RNA -

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Basic information

Entry
Database: PDB / ID: 5sup
TitleCrystal structure of the Sub2-Yra1 complex in association with RNA
Components
  • ATP-dependent RNA helicase SUB2
  • RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
  • RNA annealing protein YRA1
KeywordsHYDROLASE/RNA / mRNA export / HYDROLASE-RNA complex
Function / homology
Function and homology information


negative regulation of RNA helicase activity / RNA helicase inhibitor activity / : / : / transcription export complex / regulation of ATP-dependent activity / mRNA 3'-end processing / subtelomeric heterochromatin formation / transcription-coupled nucleotide-excision repair / mRNA export from nucleus ...negative regulation of RNA helicase activity / RNA helicase inhibitor activity / : / : / transcription export complex / regulation of ATP-dependent activity / mRNA 3'-end processing / subtelomeric heterochromatin formation / transcription-coupled nucleotide-excision repair / mRNA export from nucleus / transcription elongation by RNA polymerase II / spliceosomal complex / 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
Yra1/Mlo3, RNA recognition motif / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Helicase conserved C-terminal domain ...Yra1/Mlo3, RNA recognition motif / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif 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 / P-loop containing nucleotide triphosphate hydrolases / Nucleotide-binding alpha-beta plait domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / RNA / RNA (> 10) / ATP-dependent RNA helicase SUB2 / RNA annealing protein YRA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRen, Y. / Schmiege, P. / 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: Derived calculations / Structure summary / Category: pdbx_struct_conn_angle / struct / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct.title / _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
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

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent RNA helicase SUB2
B: ATP-dependent RNA helicase SUB2
C: ATP-dependent RNA helicase SUB2
G: RNA annealing protein YRA1
H: RNA annealing protein YRA1
I: RNA annealing protein YRA1
D: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
E: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
F: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,62118
Polymers158,0699
Non-polymers1,5539
Water48627
1
A: ATP-dependent RNA helicase SUB2
H: RNA annealing protein YRA1
D: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2076
Polymers52,6903
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-43 kcal/mol
Surface area18130 Å2
MethodPISA
2
B: ATP-dependent RNA helicase SUB2
G: RNA annealing protein YRA1
F: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2076
Polymers52,6903
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-39 kcal/mol
Surface area18180 Å2
MethodPISA
3
C: ATP-dependent RNA helicase SUB2
I: RNA annealing protein YRA1
E: RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2076
Polymers52,6903
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-41 kcal/mol
Surface area17670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.346, 99.346, 247.469
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Protein/peptide / RNA chain , 3 types, 9 molecules ABCGHIDEF

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


Mass: 44462.867 Da / Num. of mol.: 3 / Fragment: residues 61-446
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SUB2, YDL084W / Production host: Escherichia coli (E. coli) / References: UniProt: Q07478, RNA helicase
#2: Protein/peptide RNA annealing protein YRA1


Mass: 3679.246 Da / Num. of mol.: 3 / Fragment: residues 200-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YRA1, YDR381W, D9481.2, D9509.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12159
#3: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')


Mass: 4547.529 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 36 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BeF3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.5
Details: 100 mM Bis-Tris (pH 5.5), 20% PEG3350, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 44413 / % possible obs: 100 % / Redundancy: 9.9 % / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTJ

1xtj


Resolution: 2.6→49.673 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.19
RfactorNum. reflection% reflection
Rfree0.2676 2235 5.03 %
Rwork0.2189 --
obs0.2213 44413 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→49.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9644 360 96 27 10127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710310
X-RAY DIFFRACTIONf_angle_d1.07613971
X-RAY DIFFRACTIONf_dihedral_angle_d18.1726285
X-RAY DIFFRACTIONf_chiral_restr0.061592
X-RAY DIFFRACTIONf_plane_restr0.0061742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.65660.421350.33622558X-RAY DIFFRACTION100
2.6566-2.71840.40571340.31012599X-RAY DIFFRACTION100
2.7184-2.78640.37921490.29512584X-RAY DIFFRACTION100
2.7864-2.86170.32221460.28272604X-RAY DIFFRACTION100
2.8617-2.94590.3491310.28112581X-RAY DIFFRACTION100
2.9459-3.0410.33741320.27752621X-RAY DIFFRACTION100
3.041-3.14960.35141420.28192596X-RAY DIFFRACTION100
3.1496-3.27570.32181460.27812622X-RAY DIFFRACTION100
3.2757-3.42480.26861230.24842650X-RAY DIFFRACTION100
3.4248-3.60530.28511380.23312612X-RAY DIFFRACTION100
3.6053-3.83110.26481480.21632626X-RAY DIFFRACTION100
3.8311-4.12670.27131250.19992664X-RAY DIFFRACTION100
4.1267-4.54180.23511320.17522660X-RAY DIFFRACTION100
4.5418-5.19840.18761590.16592655X-RAY DIFFRACTION100
5.1984-6.5470.26521580.19692689X-RAY DIFFRACTION100
6.547-49.6820.19031370.17612857X-RAY DIFFRACTION100

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