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- PDB-4a4z: CRYSTAL STRUCTURE OF THE S. CEREVISIAE DEXH HELICASE SKI2 BOUND T... -

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Basic information

Entry
Database: PDB / ID: 4a4z
TitleCRYSTAL STRUCTURE OF THE S. CEREVISIAE DEXH HELICASE SKI2 BOUND TO AMPPNP
ComponentsANTIVIRAL HELICASE SKI2
KeywordsHYDROLASE / ATPASE / MRNA DEGRADATION / EXOSOME
Function / homology
Function and homology information


Ski complex / mRNA decay by 3' to 5' exoribonuclease / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / mRNA catabolic process / regulation of translation / defense response to virus / RNA helicase activity / RNA helicase ...Ski complex / mRNA decay by 3' to 5' exoribonuclease / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / mRNA catabolic process / regulation of translation / defense response to virus / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Sec63 N-terminal domain-like fold - #30 / : / Ski2, beta-barrel domain / Ski2, N-terminal domain / Ski2 N-terminal region / Sec63 N-terminal domain-like fold / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal ...Sec63 N-terminal domain-like fold - #30 / : / Ski2, beta-barrel domain / Ski2, N-terminal domain / Ski2 N-terminal region / Sec63 N-terminal domain-like fold / Mtr4-like, beta-barrel domain / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Antiviral helicase SKI2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsHalbach, F. / Rode, M. / Conti, E.
CitationJournal: RNA / Year: 2012
Title: The Crystal Structure of S. Cerevisiae Ski2, a Dexh Helicase Associated with the Cytoplasmic Functions of the Exosome.
Authors: Halbach, F. / Rode, M. / Conti, E.
History
DepositionOct 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Nov 6, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software / Item: _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIVIRAL HELICASE SKI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6986
Polymers113,9441
Non-polymers7545
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.794, 118.551, 129.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANTIVIRAL HELICASE SKI2 / SKI2 / SUPERKILLER PROTEIN 2


Mass: 113943.875 Da / Num. of mol.: 1 / Fragment: RESIDUES 296-1287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P35207, RNA helicase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.8 Å3/Da / Density % sol: 56.2 % / Description: NONE
Crystal growpH: 7
Details: 3% (W/V) PEG3350, 0.1M HEPES PH 7.0, 5% (V/V) ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.988
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.4→119 Å / Num. obs: 50510 / % possible obs: 99.9 % / Observed criterion σ(I): 3.1 / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.4→39.43 Å / SU ML: 0.76 / σ(F): 0 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 2563 5.1 %
Rwork0.2384 --
obs0.2402 50434 99.79 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.08 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-24.0113 Å20 Å20 Å2
2---0.8373 Å20 Å2
3----5.0356 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6503 0 47 133 6683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036665
X-RAY DIFFRACTIONf_angle_d0.6359059
X-RAY DIFFRACTIONf_dihedral_angle_d12.8722340
X-RAY DIFFRACTIONf_chiral_restr0.0381070
X-RAY DIFFRACTIONf_plane_restr0.0021160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44620.36241360.30252640X-RAY DIFFRACTION100
2.4462-2.49610.30841260.29622639X-RAY DIFFRACTION100
2.4961-2.55040.32861260.28062629X-RAY DIFFRACTION100
2.5504-2.60970.31511500.27612607X-RAY DIFFRACTION100
2.6097-2.67490.30841510.26482656X-RAY DIFFRACTION100
2.6749-2.74720.31831470.27152628X-RAY DIFFRACTION100
2.7472-2.8280.3041480.24772614X-RAY DIFFRACTION100
2.828-2.91930.28731510.24912612X-RAY DIFFRACTION100
2.9193-3.02360.31651490.25782643X-RAY DIFFRACTION100
3.0236-3.14460.33221420.26122661X-RAY DIFFRACTION100
3.1446-3.28770.33091430.25732654X-RAY DIFFRACTION100
3.2877-3.46090.26851460.25272635X-RAY DIFFRACTION100
3.4609-3.67760.28741500.25422628X-RAY DIFFRACTION100
3.6776-3.96130.26671360.22632697X-RAY DIFFRACTION100
3.9613-4.35950.21271410.19862679X-RAY DIFFRACTION100
4.3595-4.98920.21971290.19052716X-RAY DIFFRACTION100
4.9892-6.28180.28971450.26542721X-RAY DIFFRACTION100
6.2818-39.43580.25811470.2252812X-RAY DIFFRACTION98
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)
11.96591.4779-0.06074.2130.03283.4831-0.1123-0.24610.2346-0.26810.19620.8202-0.5401-0.6312-0.11390.40980.1842-0.11180.42280.10080.573855.327113.604336.9404
22.19652.1444-0.73554.5026-1.50962.6752-0.31040.07820.0328-0.5060.2377-0.17470.02820.04580.03260.1835-0.07050.03960.20370.0150.16178.6413.814656.6543
31.13520.7413-0.11482.65370.62471.5341-0.21270.13470.2695-0.31750.18390.1662-0.71410.10380.04250.50440.0165-0.08630.37810.01990.337762.7096-0.81922.4752
45.97510.223-0.80912.02720.30010.1644-0.08481.08220.308-0.26680.0466-0.6528-0.13860.1343-0.01930.1107-0.0612-0.07081.44190.19290.897378.221415.78590.6607
51.82510.0024-0.48351.4904-0.06740.7635-0.40170.7045-0.16580.32210.1909-0.2727-0.1692-0.4519-0.19170.5550.64470.68551.08990.37771.2783113.437513.084811.3395
64.31150.49020.49082.90680.92040.3185-0.17490.3563-0.418-0.4112-0.1573-0.12640.50230.12180.27440.63340.12090.04072.17310.16130.5986.614210.75842.4502
71.26450.53951.10542.02031.63615.51560.33880.0186-0.21950.2210.0342-0.14450.68350.0539-0.23360.195-0.0049-0.0130.15120.02990.249467.7261-18.266741.9381
80.0832-0.1109-0.01420.15230.02290.0055-0.0684-0.06090.00720.0501-0.06840.08840.00350.0502-0.07091.17180.33330.19220.6685-0.03921.041862.307921.901947.4398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 299:503)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 504:797)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 798:840)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 841:856)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 869:1049)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 1063:1078)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 1087:1287)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 2288)

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