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- PDB-4a4k: Crystal structure of the S. cerevisiae Ski2 insertion domain -

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Basic information

Entry
Database: PDB / ID: 4a4k
TitleCrystal structure of the S. cerevisiae Ski2 insertion domain
ComponentsANTIVIRAL HELICASE SKI2
KeywordsHYDROLASE / DEXH HELICASE / RNA DEGRADATION / EXOSOME
Function / homology
Function and homology information


mRNA decay by 3' to 5' exoribonuclease / Ski complex / nuclear-transcribed mRNA catabolic process, non-stop decay / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / regulation of translation / defense response to virus / RNA helicase activity / RNA helicase ...mRNA decay by 3' to 5' exoribonuclease / Ski complex / nuclear-transcribed mRNA catabolic process, non-stop decay / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / mRNA catabolic process / nuclear-transcribed 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
SH3 type barrels. - #1160 / YheA-like fold - #20 / YheA-like fold / : / Ski2, beta-barrel domain / Ski2, N-terminal domain / Ski2 N-terminal region / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : ...SH3 type barrels. - #1160 / YheA-like fold - #20 / YheA-like fold / : / Ski2, beta-barrel domain / Ski2, N-terminal domain / Ski2 N-terminal region / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / SH3 type barrels. / 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 / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Antiviral helicase SKI2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 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 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other
Revision 1.2Nov 6, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software / Item: _pdbx_database_status.status_code_sf
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
C: ANTIVIRAL HELICASE SKI2
E: ANTIVIRAL HELICASE SKI2
G: ANTIVIRAL HELICASE SKI2
I: ANTIVIRAL HELICASE SKI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,87610
Polymers148,5495
Non-polymers3275
Water00
1
A: ANTIVIRAL HELICASE SKI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7752
Polymers29,7101
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: ANTIVIRAL HELICASE SKI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7752
Polymers29,7101
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: ANTIVIRAL HELICASE SKI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7752
Polymers29,7101
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: ANTIVIRAL HELICASE SKI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7752
Polymers29,7101
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
I: ANTIVIRAL HELICASE SKI2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7752
Polymers29,7101
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)230.463, 123.139, 153.201
Angle α, β, γ (deg.)90.00, 131.05, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 838:1080 )
211CHAIN C AND (RESSEQ 838:1080 )
311CHAIN E AND (RESSEQ 838:1080 )
411CHAIN E AND (RESSEQ 838:1080 )
511CHAIN I AND (RESSEQ 838:1080 )

NCS oper:
IDCodeMatrixVector
1given(0.0133, 0.3863, 0.9223), (0.3772, -0.8561, 0.3531), (0.926, 0.3432, -0.1571)-57.2039, -21.5246, 72.1635
2given(-0.5868, 0.704, 0.4001), (0.7103, 0.2104, 0.6717), (0.3887, 0.6784, -0.6235)-74.5246, -9.8816, 97.6431
3given(0.6433, -0.6925, -0.3266), (0.6983, 0.3557, 0.6211), (-0.3139, -0.6276, 0.7124)-28.6697, -6.5261, 15.3845
4given(-0.0165, -0.4606, 0.8874), (-0.4666, -0.7814, -0.4143), (0.8843, -0.4209, -0.202)-46.4232, -20.792, 40.687

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Components

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


Mass: 29709.832 Da / Num. of mol.: 5 / Fragment: RESIDUES 835-1085
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD PLYSS / References: UniProt: P35207, RNA helicase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn

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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: 5.41 Å3/Da / Density % sol: 77.3 % / Description: NONE
Crystal growpH: 6.5 / Details: 3.5 M SODIUM FORMATE, 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 3.25→96 Å / Num. obs: 50807 / % possible obs: 99.6 % / Observed criterion σ(I): 1.5 / Redundancy: 2.9 % / Biso Wilson estimate: 98.25 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.4
Reflection shellResolution: 3.25→3.43 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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Processing

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

Resolution: 3.25→57.159 Å / SU ML: 0.94 / σ(F): 0 / Phase error: 27.41 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2565 2577 5.1 %
Rwork0.2359 --
obs0.237 50773 99.52 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 89.779 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 113 Å2
Baniso -1Baniso -2Baniso -3
1-2.4347 Å20 Å2-22.0356 Å2
2--4.3694 Å20 Å2
3----0.7124 Å2
Refinement stepCycle: LAST / Resolution: 3.25→57.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9084 0 5 0 9089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0019272
X-RAY DIFFRACTIONf_angle_d0.35412666
X-RAY DIFFRACTIONf_dihedral_angle_d6.2333205
X-RAY DIFFRACTIONf_chiral_restr0.0241513
X-RAY DIFFRACTIONf_plane_restr0.0021658
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A9104X-RAY DIFFRACTIONPOSITIONAL
12C9104X-RAY DIFFRACTIONPOSITIONAL0.19
13E3856X-RAY DIFFRACTIONPOSITIONAL0.34
14E9104X-RAY DIFFRACTIONPOSITIONAL0.15
15I9104X-RAY DIFFRACTIONPOSITIONAL0.15
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.31250.38191410.36272663X-RAY DIFFRACTION99
3.3125-3.38010.35511360.33862688X-RAY DIFFRACTION100
3.3801-3.45360.33871380.31772679X-RAY DIFFRACTION100
3.4536-3.53390.34361380.31442690X-RAY DIFFRACTION100
3.5339-3.62230.29671350.29342681X-RAY DIFFRACTION100
3.6223-3.72020.33161450.27982663X-RAY DIFFRACTION100
3.7202-3.82970.29681430.27062676X-RAY DIFFRACTION100
3.8297-3.95330.27461420.27932679X-RAY DIFFRACTION100
3.9533-4.09450.2631410.23662690X-RAY DIFFRACTION100
4.0945-4.25840.23441540.2192672X-RAY DIFFRACTION100
4.2584-4.45210.20811420.19342655X-RAY DIFFRACTION100
4.4521-4.68680.22831380.19282687X-RAY DIFFRACTION100
4.6868-4.98020.22251530.1972670X-RAY DIFFRACTION100
4.9802-5.36450.2581540.22452666X-RAY DIFFRACTION100
5.3645-5.90390.26791510.25452697X-RAY DIFFRACTION100
5.9039-6.7570.2861490.26932665X-RAY DIFFRACTION99
6.757-8.50860.23911350.20562696X-RAY DIFFRACTION99
8.5086-57.16820.20891420.19822679X-RAY DIFFRACTION96
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)
12.3376-0.9991-1.79992.33341.47311.6473-0.032-0.4547-0.3340.07120.00180.20240.4988-0.0277-0.08370.5283-0.0166-0.05950.68970.09160.5408-19.0098-13.659163.7978
21.97211.94981.30633.17981.89213.194-0.0241-0.16620.06480.255-0.1074-0.3030.24490.1840.09870.616-0.0663-0.06851.00950.08740.6903-25.02254.516582.0649
33.6076-0.10810.09541.41120.61612.634-0.0953-0.1913-0.18020.6033-0.1508-0.00330.8781-0.31030.09150.74780.03580.07610.69680.15680.5807-27.3726-12.06671.4745
41.8713-0.6723-0.96642.65621.03342.9338-0.0483-0.2245-0.0713-0.5354-0.09110.6311-0.49960.60730.15450.5758-0.0007-0.1480.5538-0.00080.62-5.72257.974841.5577
51.65760.24831.35144.55961.16812.67810.0440.01540.11950.33050.2585-0.66720.08320.3513-0.24640.6592-0.0351-0.02750.7289-0.15070.572718.1943-6.485836.5496
61.85020.6198-0.16552.45410.21391.5694-0.23140.46930.6051-0.97490.10080.1739-0.47720.0094-0.06990.7243-0.10430.16030.5495-0.10090.41814.10143.473331.1564
74.6086-1.41290.69420.64910.18710.70550.57660.78161.1439-0.2235-0.253-0.3505-0.0387-0.36140.01630.67130.0748-0.03090.8630.25310.9716-39.76316.079139.4695
83.2583-1.35060.44841.87441.64172.6036-0.46630.51562.2695-0.46760.4207-0.0448-0.8553-0.2154-0.07671.02320.04110.06830.88570.37412.0366-26.553628.500739.3577
93.8398-0.7481-1.53931.85750.40521.0526-0.41241.19970.7222-0.87840.31910.3705-0.1207-0.709-0.04210.55310.1664-0.11521.20390.32170.6871-39.203115.459233.5798
106.65244.165-1.16617.9968-1.54925.7253-0.76370.2614-0.064-0.65160.4071-0.53330.8770.8059-0.19851.04650.0008-0.18550.64450.04060.4726-2.905-39.0316.3353
111.2141-0.89640.70391.6259-1.24232.66340.04810.1522-0.3513-0.0320.07510.00750.6742-0.4097-0.10420.6428-0.02470.07150.6810.04580.7931-13.1875-40.553649.5221
122.4185-0.8605-1.66333.25531.44064.66460.15650.55-0.6967-0.39260.05970.69350.895-1.2214-0.34460.7039-0.086-0.01430.7293-0.06610.6819-20.6388-37.572734.9457
132.5067-0.05080.36481.18230.09683.4321-0.4684-0.48480.284-0.1263-0.07440.0049-0.19750.82940.44640.7030.058-0.0840.6214-0.00520.623917.27-27.555420.3444
142.1939-0.5890.77863.8483-0.61674.06990.23050.0638-0.1694-0.122-0.071-0.15560.68720.584-0.09320.79890.1111-0.07140.82580.11920.616524.2447-44.5701-0.6997
151.0121-0.07550.08410.5789-1.54714.9525-0.22690.34750.32880.373-0.0122-0.5432-0.43460.30630.34490.5999-0.0703-0.15480.7013-0.00340.476822.1836-27.211311.8606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 837:888)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 889:1016)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 1017:1082)
4X-RAY DIFFRACTION4(CHAIN C AND RESID 837:880)
5X-RAY DIFFRACTION5(CHAIN C AND RESID 881:1014)
6X-RAY DIFFRACTION6(CHAIN C AND RESID 1015:1082)
7X-RAY DIFFRACTION7(CHAIN E AND RESID 838:907)
8X-RAY DIFFRACTION8(CHAIN E AND RESID 908:1014)
9X-RAY DIFFRACTION9(CHAIN E AND RESID 1015:1081)
10X-RAY DIFFRACTION10(CHAIN G AND RESID 837:857)
11X-RAY DIFFRACTION11(CHAIN G AND RESID 858:1020)
12X-RAY DIFFRACTION12(CHAIN G AND RESID 1021:1082)
13X-RAY DIFFRACTION13(CHAIN I AND RESID 838:880)
14X-RAY DIFFRACTION14(CHAIN I AND RESID 881:1033)
15X-RAY DIFFRACTION15(CHAIN I AND RESID 1034:1082)

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