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- PDB-7am1: Structure of yeast Ssd1, a pseudonuclease -

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Basic information

Entry
Database: PDB / ID: 7am1
TitleStructure of yeast Ssd1, a pseudonuclease
ComponentsProtein SSD1
KeywordsRNA BINDING PROTEIN / stress response / Ssd1 / pseudonuclease / RNB family
Function / homology
Function and homology information


regulation of fungal-type cell wall organization / cellular bud / exosome (RNase complex) / intracellular mRNA localization / cellular bud neck / regulation of G1 to G0 transition / mRNA catabolic process / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / P-body ...regulation of fungal-type cell wall organization / cellular bud / exosome (RNase complex) / intracellular mRNA localization / cellular bud neck / regulation of G1 to G0 transition / mRNA catabolic process / mRNA regulatory element binding translation repressor activity / mRNA 3'-UTR binding / P-body / mRNA 5'-UTR binding / cytoplasmic stress granule / 3'-5'-RNA exonuclease activity / negative regulation of translation / cell cycle / cell division / mRNA binding / nucleus / cytoplasm
Similarity search - Function
DIS3-like exonuclease 2, C-terminal / DIS3-like exonuclease 2 C terminal / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCook, A.G. / Jayachandran, U.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust200898/Z/16/Z United Kingdom
Citation
Journal: Nucleic Acids Res. / Year: 2022
Title: Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site.
Authors: Bayne, R.A. / Jayachandran, U. / Kasprowicz, A. / Bresson, S. / Tollervey, D. / Wallace, E.W.J. / Cook, A.G.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W.
History
DepositionOct 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SSD1
B: Protein SSD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,6148
Polymers206,3012
Non-polymers1,3146
Water10,142563
1
A: Protein SSD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8654
Polymers103,1501
Non-polymers7153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein SSD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7494
Polymers103,1501
Non-polymers5993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.463, 74.003, 106.467
Angle α, β, γ (deg.)91.274, 91.802, 117.647
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVAL(chain 'A' and ((resid 338 through 339 and (name N...AA338 - 4134 - 79
12ASNASNLEULEU(chain 'A' and ((resid 338 through 339 and (name N...AA485 - 490151 - 156
13ARGARGGLUGLU(chain 'A' and ((resid 338 through 339 and (name N...AA500 - 527166 - 193
14LYSLYSLEULEU(chain 'A' and ((resid 338 through 339 and (name N...AA536 - 561202 - 227
15PROPROPHEPHE(chain 'A' and ((resid 338 through 339 and (name N...AA579 - 1144245 - 810
16SERSERPROPRO(chain 'A' and ((resid 338 through 339 and (name N...AA1146 - 1187812 - 853
17GLNGLNMETMET(chain 'A' and ((resid 338 through 339 and (name N...AA1194 - 1247860 - 913
28SERSERVALVAL(chain 'B' and (resid 338 through 348 or (resid 349...BB338 - 4134 - 79
29ASNASNLEULEU(chain 'B' and (resid 338 through 348 or (resid 349...BB485 - 490151 - 156
210ARGARGGLUGLU(chain 'B' and (resid 338 through 348 or (resid 349...BB500 - 527166 - 193
211LYSLYSLEULEU(chain 'B' and (resid 338 through 348 or (resid 349...BB536 - 561202 - 227
212PROPROPHEPHE(chain 'B' and (resid 338 through 348 or (resid 349...BB579 - 1144245 - 810
213SERSERPROPRO(chain 'B' and (resid 338 through 348 or (resid 349...BB1146 - 1187812 - 853
214GLNGLNMETMET(chain 'B' and (resid 338 through 348 or (resid 349...BB1194 - 1247860 - 913

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Components

#1: Protein Protein SSD1 / Protein SRK1


Mass: 103150.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SSD1, CLA1, RLD1, SRK1, YDR293C, D9819.4 / Plasmid: pEC / Details (production host): pET-based vector / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24276
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 50 mM Tris-HCl pH 8.0, 25% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.9→61.46 Å / Num. obs: 144175 / % possible obs: 98 % / Redundancy: 2.7 % / Biso Wilson estimate: 37.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.044 / Rrim(I) all: 0.076 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.986-106.3222.690.02926.77579720.99820.0210.03697.54
3.958-4.9862.760.03225.2278960.99770.0220.0496.45
3.457-3.9582.540.03819.85478580.99710.0270.04796.08
3.141-3.4572.730.05115.70578790.9960.0360.06396.32
2.916-3.1412.780.08211.97179080.99440.0470.08296.64
2.744-2.9162.810.0899.20679380.9910.0610.10897.2
2.607-2.7442.60.1097.08979830.98710.0780.13597.37
2.493-2.6072.540.1335.70478940.98060.0960.16496.99
2.397-2.4932.710.1634.97379430.9750.1150.20196.96
2.314-2.3972.730.2094.00779190.96440.1480.25897.42
2.242-2.3142.750.2483.42779550.95510.1750.30596.95
2.178-2.2422.760.2912.96279180.93650.2060.35997.07
2.121-2.1782.790.3612.52279490.90720.2550.44497
2.069-2.1212.630.4551.86879870.86460.3280.56496.87
2.022-2.0692.630.5731.5178840.79390.4160.71296.52
1.979-2.0222.520.6841.23678690.71760.5040.85496.59
1.939-1.9792.660.9080.98878950.64750.6571.12796.78
1.903-1.9392.691.1010.83179430.55790.7971.36696.76

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VNU, 4PMW

2vnu

4pmw


Resolution: 1.9→61.46 Å / SU ML: 0.2603 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.097 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2239 7109 4.99 %
Rwork0.205 135250 -
obs0.206 142359 96.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.97 Å2
Refinement stepCycle: LAST / Resolution: 1.9→61.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12398 0 43 563 13004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003612680
X-RAY DIFFRACTIONf_angle_d0.655817246
X-RAY DIFFRACTIONf_chiral_restr0.04482033
X-RAY DIFFRACTIONf_plane_restr0.00372234
X-RAY DIFFRACTIONf_dihedral_angle_d12.19677718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.43312140.46624530X-RAY DIFFRACTION96.4
1.92-1.950.44091950.43134484X-RAY DIFFRACTION95.63
1.95-1.970.40971830.41784513X-RAY DIFFRACTION96.84
1.97-20.38171910.39014573X-RAY DIFFRACTION96.63
2-2.020.38412130.36934536X-RAY DIFFRACTION96.68
2.02-2.050.39062280.3434550X-RAY DIFFRACTION96.27
2.05-2.080.34352230.32494497X-RAY DIFFRACTION96.76
2.08-2.110.33542380.30254502X-RAY DIFFRACTION96.6
2.11-2.140.30392050.27424531X-RAY DIFFRACTION97.15
2.14-2.180.27282420.2634560X-RAY DIFFRACTION96.76
2.18-2.220.26472260.25914459X-RAY DIFFRACTION97.36
2.22-2.260.25192010.25164616X-RAY DIFFRACTION96.9
2.26-2.30.28092320.24734497X-RAY DIFFRACTION96.97
2.3-2.350.27652380.23094484X-RAY DIFFRACTION96.98
2.35-2.40.27492430.22774565X-RAY DIFFRACTION97.19
2.4-2.450.25812130.20784515X-RAY DIFFRACTION96.91
2.45-2.510.23442090.20744563X-RAY DIFFRACTION97.05
2.51-2.580.26082270.20334519X-RAY DIFFRACTION96.72
2.58-2.660.23573000.20394528X-RAY DIFFRACTION97.38
2.66-2.740.23592970.20544422X-RAY DIFFRACTION97.12
2.74-2.840.24952850.20834475X-RAY DIFFRACTION97.16
2.84-2.960.25493010.2164458X-RAY DIFFRACTION96.89
2.96-3.090.23832970.21044437X-RAY DIFFRACTION96.71
3.09-3.250.22012820.20124457X-RAY DIFFRACTION96.58
3.25-3.460.23852080.19614507X-RAY DIFFRACTION96.17
3.46-3.720.19152430.17884456X-RAY DIFFRACTION95.66
3.72-4.10.16622550.16174508X-RAY DIFFRACTION96.51
4.1-4.690.15312980.13844394X-RAY DIFFRACTION96.54
4.69-5.910.18332020.16214555X-RAY DIFFRACTION96.82
5.91-61.460.19662200.18684559X-RAY DIFFRACTION97.37
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)
11.69596124998-0.951596915815-0.0790858362552.226730520220.4245703683781.47960539595-0.2448978237660.03503364580040.0649164716090.4945063643010.202006771181-0.1029582523490.4325736542360.0982212973427-0.06305128739790.6404882741820.0576012083211-0.05219723164890.369426399556-0.02359549273620.42682749951821.3172720627-86.7184094368-69.9207662074
20.335876869524-0.05173931045320.4208640908121.079023856820.6457772248241.519729325720.09584628623430.121351765381-0.291396933930.0667692936060.0761786757147-0.5882738096620.1954823986240.327274104101-0.1211673092470.4140181191370.0448673667615-0.03721626885590.476002745044-0.04712513794980.57891060762830.745625076-79.9127723016-90.0747807638
30.636538232417-0.232332155061-0.1583902528361.503195810020.5782614491291.5071748703-0.153493270992-0.06106267600110.08680335676190.2179356900170.0766209416852-0.0015858529806-0.224659704822-0.0553844335660.0827958565910.4408089625030.0406782976899-0.05578743299330.322486949239-0.01971507682340.3663813647413.7001922363-54.5036212513-67.3822008307
4-0.0699478169547-0.439840045222-0.147301141431.037959880580.4506807757141.8039828036-0.00905595178817-0.0157861503104-0.03985295345360.04986254628630.00944677555961-0.0365133316833-0.0454113214460.04601528371950.01604196346210.335090709563-0.0171709302556-0.02688720158580.355982639219-0.009973067963470.36815861361717.3881108597-71.5994631031-85.1364046851
51.36082570589-0.105473854652-0.1175267860441.19959496672-0.007522879807822.35680454339-0.03756621365360.144341378902-0.0175020498257-0.2027145877330.0467957887257-0.1374463101880.1492576993280.408355343589-0.076277766020.496137527098-0.007682995678940.04459700361560.488195958274-0.06342479491380.42457270262128.0860373422-79.1541839231-105.099654556
61.514751088380.107952876875-0.3716015107091.204422480780.534457625322.111410365050.006504643984580.1784914579430.0790275911161-0.455979276037-0.05781265643650.00965671717246-0.191859774253-0.08374638128870.03276613325050.4547610708130.00637442188088-0.04396858056140.378883116326-0.01076981585680.35408930069914.0441155182-70.9086180655-102.848132791
72.04549772045-0.8004208334760.2839637879592.11830069309-0.08763793667461.18739668191-0.0924653202190.155475924950.1615595592570.05425483566490.0234340140425-0.1042087967490.2888731123750.150470458431-0.09959920994470.436049479587-0.0256443745222-0.04559558030380.3399233293390.004969570752330.39436949700434.9396046415-57.6443960337-16.9381771112
80.945286854767-0.133747245962-0.05761623786811.119041523440.1368945123071.21117102466-0.0161132759976-0.0216763728720.04295397940370.03457797705180.007067600725650.087436862191-0.131879043875-0.04580649025360.04791862806320.357488452923-0.00853450359325-0.0405718105060.3038558184170.006794999910480.37523439335127.0594071615-25.5436266119-13.2872817246
9-0.03343811436580.182397925836-0.3032411329591.229001994620.2325632206661.98618146596-0.0534915492183-0.0241685660222-0.076134219756-0.2986742866080.0227651788273-0.09159482343320.2564577078610.262180304267-0.07669234759840.4739081072540.0532288597605-0.01510752230180.392021727950.01228687783430.36718029058738.4929179612-42.798773757-37.8156248311
101.196970934670.567038340008-0.4875381577320.7377798101160.2784132985051.9207973548-0.1458291008130.1478709797870.0967241366921-0.5488227199280.07601331994480.09932508437950.0723231283681-0.10220063652-0.03349013798990.7162426507860.0142429354225-0.06802464920280.4454210003760.01265926050590.42553031311932.9273639738-38.9358397106-49.7693213498
11-0.01588652293280.1279641792950.1266257703930.8137513949240.9819521350521.918639143850.249381657620.021112399366-0.310300740032-0.256348587696-0.116998542374-0.4355456098480.3543770893140.353656432383-0.1866920082260.5864992155170.1118899885940.06719206911520.5185543452290.05174119703440.52290524626347.8960292523-48.5588192304-34.4012621999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 336 through 413 ) or chain 'A' and (resid 541 through 675)
2X-RAY DIFFRACTION2chain 'A' and (resid 414 through 540 )
3X-RAY DIFFRACTION3chain 'A' and (resid 676 through 1022 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1023 through 1097 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1098 through 1135 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1136 through 1248 )
7X-RAY DIFFRACTION7chain 'B' and (resid 338 through 415 ) or chain 'B' and (resid 541 through 675)
8X-RAY DIFFRACTION8chain 'B' and (resid 676 through 1022 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1023 through 1135 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1136 through 1249 )
11X-RAY DIFFRACTION11chain 'B' and (resid 416 through 540)

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