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- PDB-7ocx: Crystal Structure of the PID-3 TOFU-6 RRM domain complex -

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Basic information

Entry
Database: PDB / ID: 7ocx
TitleCrystal Structure of the PID-3 TOFU-6 RRM domain complex
Components
  • Embryonic developmental protein tofu-6
  • Protein pid-3
KeywordsRNA BINDING PROTEIN / piRNA biogenesis 21U RNA RNA recognition motif RNA binding
Function / homology
Function and homology information


21U-RNA metabolic process / positive regulation of chromosome segregation / RNA cap binding complex / piRNA processing / mitotic sister chromatid separation / embryonic cleavage / embryo development ending in birth or egg hatching / positive regulation of cell division / chromosome segregation / DNA replication ...21U-RNA metabolic process / positive regulation of chromosome segregation / RNA cap binding complex / piRNA processing / mitotic sister chromatid separation / embryonic cleavage / embryo development ending in birth or egg hatching / positive regulation of cell division / chromosome segregation / DNA replication / cell division / perinuclear region of cytoplasm / RNA binding / nucleus / cytoplasm
Similarity search - Function
RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein pid-3 / Embryonic developmental protein tofu-6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsBasquin, J. / Ketting, R.F. / Falk, S.
CitationJournal: Genes Dev. / Year: 2021
Title: Structural basis of PETISCO complex assembly during piRNA biogenesis in C. elegans .
Authors: Perez-Borrajero, C. / Podvalnaya, N. / Holleis, K. / Lichtenberger, R. / Karaulanov, E. / Simon, B. / Basquin, J. / Hennig, J. / Ketting, R.F. / Falk, S.
History
DepositionApr 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein pid-3
B: Protein pid-3
C: Embryonic developmental protein tofu-6
D: Embryonic developmental protein tofu-6


Theoretical massNumber of molelcules
Total (without water)41,1044
Polymers41,1044
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-18 kcal/mol
Surface area16770 Å2
Unit cell
Length a, b, c (Å)43.980, 68.002, 130.585
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Protein pid-3 / piRNA biogenesis and chromosome segregation protein 1 / piRNA-induced silencing defective protein 3


Mass: 9160.454 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: pid-3, pics-1, Y23H5A.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76616
#2: Protein Embryonic developmental protein tofu-6 / 21U-RNA biogenesis fouled up protein 6 / Maternal effect lethal protein 47


Mass: 11391.714 Da / Num. of mol.: 2
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 BL21(DE3) (bacteria) / References: UniProt: Q09293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium acetate pH 5.0 0.2 M Sodium chloride 17 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00, 1.54
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.541
ReflectionResolution: 1.7→41.68 Å / Num. obs: 43394 / % possible obs: 97.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 33.62 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0855 / Rpim(I) all: 0.02472 / Net I/σ(I): 16.24
Reflection shellResolution: 1.7→1.761 Å / Mean I/σ(I) obs: 0.56 / Num. unique obs: 3808 / CC1/2: 0.171 / CC star: 0.541

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→41.68 Å / SU ML: 0.2701 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.0833
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2317 2157 5.01 %
Rwork0.194 40895 -
obs0.1958 43052 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 0 139 2710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872629
X-RAY DIFFRACTIONf_angle_d1.09243562
X-RAY DIFFRACTIONf_chiral_restr0.0616395
X-RAY DIFFRACTIONf_plane_restr0.0106470
X-RAY DIFFRACTIONf_dihedral_angle_d5.773355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.51561100.48492058X-RAY DIFFRACTION75.86
1.74-1.780.39641380.39752580X-RAY DIFFRACTION93.79
1.78-1.830.35731450.32692759X-RAY DIFFRACTION99.97
1.83-1.890.31471440.29012747X-RAY DIFFRACTION99.93
1.89-1.950.33641430.27742722X-RAY DIFFRACTION99.97
1.95-2.020.26031450.24352765X-RAY DIFFRACTION99.76
2.02-2.10.26521450.21272750X-RAY DIFFRACTION99.9
2.1-2.190.26311460.19382764X-RAY DIFFRACTION99.97
2.19-2.310.25551450.19352752X-RAY DIFFRACTION99.83
2.31-2.450.24821470.18922781X-RAY DIFFRACTION99.93
2.45-2.640.24531450.20832763X-RAY DIFFRACTION99.93
2.64-2.910.25661480.19582805X-RAY DIFFRACTION99.97
2.91-3.330.21651480.19232799X-RAY DIFFRACTION100
3.33-4.190.19631510.16082854X-RAY DIFFRACTION99.97
4.19-41.680.19561570.17232996X-RAY DIFFRACTION99.87
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)
12.854380616491.86417818723-0.6133050068832.731928479232.50391993187.15826925412-0.0007120599097690.118127409759-0.0597231204008-0.169304564930.213364505729-0.4763905020710.01514195797550.447583352564-0.2439996422590.2761253062090.06649882670470.02893026657780.268594824013-0.01763616355930.41099987733735.145704646130.827153914258.9001037448
22.150036770310.09678363648610.01897324438741.82046280451-1.005704482264.846585597880.06794892190630.064954664165-0.214227231299-0.1753195775660.0470912162689-0.01804606314870.5186543659840.0790683951724-0.1064963168640.322464390750.0344691064621-0.03782824278170.216064926909-0.02727834452340.40329808478532.996734723722.366817280864.1840091596
32.481023999220.1985485676910.8225071124768.94223171728-2.810482653615.1992144607-0.02492625828250.1442637166690.180176361734-0.879866536270.04827760003850.1364458131110.122439745896-0.29105202622-0.00257945712380.309450519891-0.00632334145447-0.05306247039640.3072294334530.001936292122570.31036537310824.489175996145.797358021743.9958664123
46.741456153612.16317998571-1.975436373684.07100380456-4.636024898977.671961987560.3534567951790.4421352452870.272733812026-0.748060358459-0.3283355651750.023813289543-0.2326168832010.451608674287-0.001031217704190.5161000623650.05342092186210.07102259306670.3214384514230.008007637905110.40491951152727.582393623847.534723666542.1470024392
52.90267049236-3.905794079612.917520439776.75545633807-3.668911861253.890409842380.4071482410810.144093249186-0.922232290135-1.33141443880.3583952028252.277819435280.356644067348-0.759631878272-0.6309521768880.62041976424-0.00709632390862-0.3130604926970.4859615240690.06628433254890.74662784641416.863489395840.971062178440.4765081852
65.92809910599-5.746377130516.604004780595.70256778456-6.529701566157.458697742110.3367064740390.5962393118330.245412737783-0.642084845359-0.577493729659-0.2267501052810.4372375421030.4833843303440.3241549983450.7685784536650.1791855264490.2303942210670.5093407145320.05399031200330.66953923012738.222307229831.279204694141.7269104927
72.108885836471.19454604282-0.3530311465813.33106900758-1.044430783883.845901683570.101272033759-0.3647738848640.07301322597081.894891545230.427280849281-0.722988846203-0.489967009347-0.0938873079938-0.4734813034680.609214170799-0.0824715734905-0.0613178016480.31964745581-0.005080391891180.43974180225726.896188496334.141190785285.0251806111
83.383662039860.066095701776-1.12507759586.80906056985-0.9071158844672.585109455120.296694281501-0.408913035988-0.2639323053320.955178522998-0.285920130019-0.6135624393180.03938545484050.038319096234-0.01053261999970.39124903329-0.0572160013244-0.131003856660.2727727992480.04876565409770.35370024841225.060443091716.803341315484.6728104512
92.58489055868-1.294473128790.8474282904912.590392576160.523760458314.606821131880.188451083611-0.814174357217-0.6899971888340.464055782432-0.8828397585060.3574459136291.31485450408-0.4240239470170.2154485305311.37525109159-0.197551249065-0.404601129480.5493343607440.1418742836650.74685054506730.556654671310.960508657798.6252551627
103.128067803242.86186180441-0.4695642178998.87846847962-5.028299714517.447923801030.5516734379430.01188906841570.1455888071741.07353250245-0.3433041523260.238721016378-0.00579685376329-0.0176840484824-0.2667489700330.416733251527-0.0528501384043-0.004066974444450.212062199284-0.03569032378290.30768279412721.237247815924.666629412484.2234849431
115.402598352592.562332387352.037638587282.287869309262.390376010295.121689453110.71516809296-0.08538889408060.5526653168242.11913037584-0.5799788117020.971036557722-0.000974764087146-0.105675195296-0.1522472944390.718931735711-0.1294544412220.1144010813490.380532988519-0.02458238755250.45988672605216.767640903719.041473757990.6047929365
127.369714739136.90158197463-5.886635056638.84560422562-6.338299544164.97589581904-0.09139099349670.3679571154990.174910252853-0.2599446487320.3320726949440.0178002977663-0.187313881001-0.139166519423-0.1425290030350.205140552506-0.00437616701165-0.01179760884920.238797928708-0.01645763459880.37909560675635.763672162750.645682708962.2242812124
132.849127831550.6468832148991.178281083843.905525674085.073041209998.529530072010.206300152755-0.131778638375-0.1344594326730.3414908680160.0900993069053-0.3144191676430.641081120260.103366746227-0.3080123626350.2636089301850.000242789696585-0.02898716207840.2107018734760.01351389418960.34271298744132.790077339737.898102053172.1668948668
142.821346396870.09635786919761.275496385751.71756203832-0.3421793768556.95499754803-0.025614822440.1980737957740.00514634252569-0.0101584107967-0.004438897964980.00426116800114-0.1209796717190.05469884512640.01995535531460.2245049738930.00528966442771-0.003915784541050.209602676013-0.01418446800160.39168053789231.462751988644.960380664462.9138185244
152.33073376641-1.75038434812.042143272994.47183326838-5.60565659986.902362098190.00895121485446-0.0767702571545-0.2479677337320.5406856233560.2328190323880.523972069128-0.213636282117-0.594540085913-0.3943943997130.3572955030930.03655246416990.07164356482720.316211417083-0.03361442691120.41865427720721.43690515842.39971316276.1950999308
163.531778645042.86538021992-3.080998217232.49634210242-2.564610825542.756716948460.387706962212-0.2053301811522.295899373410.1668075187170.539202845540.672429133429-0.4243098885530.156444355568-1.003079592810.354902932560.01977675716480.05370147553150.3368280627630.008351114106850.69999795109829.938924953853.453628076866.1973434809
170.1369629448610.735968537315-0.9074128633944.51569476275-5.564896365466.84076895218-0.4757439771520.201478993976-0.2024826228442.411644283450.262272846879-0.840212079374-2.28376238556-1.27317047920.3018500966250.7817706453410.154672535229-0.129791885020.6420258906920.02985761189270.70705016480846.707502195424.518118361572.3465208334
186.0297729223-3.178641984864.228152008237.54268286946-4.551673205144.141159367440.1457551398360.428795153558-0.252354234556-0.378027661022-0.321894867003-0.4655548102890.8620728227621.600147456210.07309802475920.4240292002890.109856136459-0.01971683063120.307695250197-0.053274764090.45064737267939.174354327618.96930561467.5746062114
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 209 through 223 )BB209 - 22316 - 30
22chain 'B' and (resid 224 through 274 )BB224 - 27431 - 81
33chain 'C' and (resid 7 through 36 )CC7 - 361 - 30
44chain 'C' and (resid 37 through 62 )CC37 - 6231 - 56
55chain 'C' and (resid 63 through 89 )CC63 - 8957 - 83
66chain 'C' and (resid 90 through 99 )CC90 - 9984 - 93
77chain 'D' and (resid 8 through 13 )DD8 - 131 - 6
88chain 'D' and (resid 14 through 44 )DD14 - 447 - 37
99chain 'D' and (resid 45 through 52 )DD45 - 5238 - 45
1010chain 'D' and (resid 53 through 72 )DD53 - 7246 - 65
1111chain 'D' and (resid 73 through 91 )DD73 - 9166 - 84
1212chain 'A' and (resid 198 through 208 )AA198 - 2081 - 11
1313chain 'A' and (resid 209 through 223 )AA209 - 22312 - 26
1414chain 'A' and (resid 224 through 256 )AA224 - 25627 - 59
1515chain 'A' and (resid 257 through 267 )AA257 - 26760 - 70
1616chain 'A' and (resid 268 through 274 )AA268 - 27471 - 77
1717chain 'B' and (resid 194 through 200 )BB194 - 2001 - 7
1818chain 'B' and (resid 201 through 208 )BB201 - 2088 - 15

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