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- PDB-9g6z: C. elegans TOFU-6 eTUDOR TOFU-1 peptide complex -

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Basic information

Entry
Database: PDB / ID: 9g6z
TitleC. elegans TOFU-6 eTUDOR TOFU-1 peptide complex
Components
  • Embryonic developmental protein tofu-6
  • Protein tofu-1
KeywordsPROTEIN BINDING / piRNA biogenesis / TUDOR domain / RNA BINDING PROTEIN
Function / homology
Function and homology information


21U-RNA metabolic process / primary piRNA processing / positive regulation of chromosome segregation / RNA cap binding complex / endoribonuclease complex / piRNA processing / mitotic sister chromatid separation / embryonic cleavage / embryo development ending in birth or egg hatching / positive regulation of cell division ...21U-RNA metabolic process / primary piRNA processing / positive regulation of chromosome segregation / RNA cap binding complex / endoribonuclease complex / piRNA processing / mitotic sister chromatid separation / embryonic cleavage / embryo development ending in birth or egg hatching / positive regulation of cell division / DNA replication / cell division / perinuclear region of cytoplasm / RNA binding / nucleus / cytoplasm
Similarity search - Function
RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Schlafen-like protein 1 / Embryonic developmental protein tofu-6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsKetting, R. / Falk, S.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science Fund10.55776 / I6110 Austria
Austrian Science Fund10.55776 / DOC177 Austria
CitationJournal: Nature / Year: 2023
Title: piRNA processing by a trimeric Schlafen-domain nuclease.
Authors: Podvalnaya, N. / Bronkhorst, A.W. / Lichtenberger, R. / Hellmann, S. / Nischwitz, E. / Falk, T. / Karaulanov, E. / Butter, F. / Falk, S. / Ketting, R.F.
History
DepositionJul 19, 2024Deposition site: PDBE / Processing site: PDBE
SupersessionDec 4, 2024ID: 8BY5
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Embryonic developmental protein tofu-6
B: Protein tofu-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8764
Polymers26,6922
Non-polymers1842
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-13 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.150, 69.202, 60.946
Angle α, β, γ (deg.)90.000, 91.473, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Embryonic developmental protein tofu-6 / 21U-RNA biogenesis fouled up protein 6 / Maternal effect lethal protein 47


Mass: 22710.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tofu-6, mel-47, EEED8.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09293
#2: Protein/peptide Protein tofu-1 / 21U-RNA biogenesis fouled up protein 1


Mass: 3981.376 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: tofu-1, C27H6.3 / Production host: Escherichia coli (E. coli) / References: UniProt: O17608
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Na bromide, 0.1 M Bis Tris propane pH 7.5, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.22→60.93 Å / Num. obs: 12063 / % possible obs: 99 % / Redundancy: 5.1 % / Biso Wilson estimate: 35.81 Å2 / CC1/2: 0.992 / Net I/σ(I): 10.3
Reflection shellResolution: 2.22→2.26 Å / Num. unique obs: 626 / CC1/2: 0.777

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→36.52 Å / SU ML: 0.3171 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2295 1212 10.06 %
Rwork0.1756 10841 -
obs0.181 12053 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.09 Å2
Refinement stepCycle: LAST / Resolution: 2.22→36.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 12 77 1762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521722
X-RAY DIFFRACTIONf_angle_d0.6712323
X-RAY DIFFRACTIONf_chiral_restr0.0422261
X-RAY DIFFRACTIONf_plane_restr0.0051294
X-RAY DIFFRACTIONf_dihedral_angle_d18.8706653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.310.31851330.25651205X-RAY DIFFRACTION98.82
2.31-2.420.27861290.22041204X-RAY DIFFRACTION99.55
2.42-2.550.2971450.20051201X-RAY DIFFRACTION99.19
2.55-2.710.28661330.20831208X-RAY DIFFRACTION99.55
2.71-2.910.29421310.22481195X-RAY DIFFRACTION99.77
2.91-3.210.25261380.18891207X-RAY DIFFRACTION99.48
3.21-3.670.21371290.16861193X-RAY DIFFRACTION98.22
3.67-4.620.17511350.13681186X-RAY DIFFRACTION96.63
4.62-36.520.20461390.15421242X-RAY DIFFRACTION99.78
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)
11.68400813655-0.715539311710.5237261474856.84469832918-4.5721238925.67695260872-0.0962347587506-0.1088490701680.372308030923-1.009919932630.2837613274930.4719171930380.402687678243-0.317289937318-0.2190827628410.437187798936-0.0725362671311-0.1389648846730.340163105393-0.07200852580930.4316847094157.89040869673.4920361876311.3643522514
22.258648094120.1358867778010.9517693922361.83224727590.3366824967182.52296616852-0.0715641176635-0.097218393401-0.09172580553050.05538841264420.134049149763-0.09533953319660.1722495985850.0466786613008-0.01040992891380.261975170058-0.0146970953929-0.02345676901570.287320752413-0.04020999793740.3547132541615.9665685733-12.032770401528.0619001279
31.83143884204-0.3903892254120.2974985365120.857060693209-0.3860484929922.23452496207-0.06377156329420.222657019169-0.253437751346-0.0577208004948-0.02120521096670.04395308932570.0290063291862-0.2554150739930.1188295457810.246838006947-0.0263743600742-0.02490682466990.294484106687-0.002532580719480.37911255371412.2376712122-1.1379346786728.5891219249
43.68038182925-0.276925166691-0.1797911353842.3009517107-0.5276646094213.657118177980.2551789133450.78220239535-0.65824576426-0.200453487930.02538164916180.01707661557580.182183411069-0.153514029309-0.1074134154710.480839931087-0.003916818541890.1166566830910.470811706242-0.1657407888840.52949466969724.007462069-6.1164988884311.0833712943
51.75174736257-0.501703844401-0.9041897155261.925749970310.09718725095832.254773093750.03743503949240.600833596092-0.24889412334-0.927357634236-0.2280159489050.140126647739-0.252067079427-0.1654809020240.1732019458160.6034732310120.03296907390120.02457476673780.4727991014060.01913939301590.3720111964812.679705185411.02278139277.14407221449
63.161364520790.1038503064060.0463284637081.96915207347-0.04630239535112.07120702652-0.1637393067510.4956126610170.302807100598-0.5439959190540.229138280203-0.50949064379-0.1979098703730.254419995477-0.09159845350740.399329933714-0.05381928164540.06810134562630.3972703277950.01159408039930.41729471686420.08372343828.0123770938812.6869321862
71.70634543903-1.47305632255-1.102353495495.936664808880.6539071896851.632194312210.1308429144340.1831476077880.320846242636-0.174096425177-0.175798320873-0.828448277323-0.1113039472860.331524306280.03548684060860.302313509205-0.05385085535580.03519969507150.2969864441-0.01855607973110.45723428716118.73700124818.0707213593420.8955711225
80.7460613663260.1841370242290.2356522268582.528148679430.1232062149111.68426942564-0.03672801808910.323068467498-0.00357460469567-0.4829345569980.160457914357-0.08288645749220.139920401584-0.258974950227-0.08783303032050.2771715414160.012047458383-0.008204390937030.326719606191-0.02156683092410.26005303515113.22982535562.0768346745119.0259326467
91.75017956709-0.28850313227-0.07187513193991.79908787647-0.1013141930672.20870994173-0.0904861653412-0.2006201668470.2262678937530.2066217855340.08199078332590.0743754671343-0.138413474151-0.07497405014670.009587743114620.2681300250610.00375791603235-0.007685083888960.274471809445-0.04662416169230.36646321054314.7384344292-3.0439367294535.9778579856
104.29548894901-1.47103147856-0.2531415990473.46777427329-0.01593608148062.11525086421-0.40926103833-0.598883053023-0.3766687669810.721683702720.28035201279-0.0310252687853-0.175474152577-0.03187145085070.09899996650230.4414167516090.0580908579996-0.04004278328330.404764374056-0.0495364649390.35682803870611.4223190161-6.8893996217945.9117954998
115.58539512991-0.8620218650061.261503747384.32314008606-1.453694720266.017100068370.208946027031-0.07570488627460.5064344231110.712353146469-0.152563011235-0.199185801867-1.439098320591.640500417250.1848943979440.6455350545590.00829950872074-0.03085955644160.928658203253-0.232292555150.53529984558319.04620200280.78990641321847.636891428
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 115 through 124 )AA115 - 1241 - 10
22chain 'A' and (resid 125 through 136 )AA125 - 13611 - 22
33chain 'A' and (resid 137 through 159 )AA137 - 15923 - 45
44chain 'A' and (resid 160 through 175 )AA160 - 17546 - 61
55chain 'A' and (resid 176 through 190 )AA176 - 19062 - 76
66chain 'A' and (resid 191 through 208 )AA191 - 20877 - 94
77chain 'A' and (resid 209 through 222 )AA209 - 22295 - 108
88chain 'A' and (resid 223 through 253 )AA223 - 253109 - 139
99chain 'A' and (resid 254 through 295 )AA254 - 295140 - 181
1010chain 'A' and (resid 296 through 314 )AA296 - 314182 - 200
1111chain 'B' and (resid 85 through 96 )BB85 - 961 - 12

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