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

ID or keywords:

Entry

Database: PDB / ID: 7ocx

Title

Crystal Structure of the PID-3 TOFU-6 RRM domain complex

Components

Embryonic developmental protein tofu-6
Protein pid-3

Keywords

RNA 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 ...
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 1.7 Å

Authors

Basquin, J. / Ketting, R.F. / Falk, S.

Citation

Journal: 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

Deposition	Apr 28, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 25, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 6, 2021	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ocx.cif.gz	238.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7ocx.ent.gz	169.7 KB	Display	PDB format
PDBx/mmJSON format	7ocx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oc/7ocx ftp://data.pdbj.org/pub/pdb/validation_reports/oc/7ocx	HTTPS FTP

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Related structure data

Related structure data	7o6lC 7o6nC 7oczC C: citing same article (ref.)
Similar structure data	5go3-2 4txy-1 3lkk-d 4txz-1 3mtj-d 4ty0-2 1ks2-d 6awg-1 4gmk-d 5go3-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein pid-3

B: Protein pid-3

C: Embryonic developmental protein tofu-6

D: Embryonic developmental protein tofu-6

41.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering

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 number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
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

#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 / Water Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.22 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1.00, 1.54

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 11, 2020

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	1.54	1

Reflection

Resolution: 1.7→41.68 Å / Num. obs: 43394 / % possible obs: 97.9 % / Redundancy: 12.7 % / B_iso Wilson estimate: 33.62 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.0855 / R_pim(I) all: 0.02472 / Net I/σ(I): 16.24

Reflection shell

Resolution: 1.7→1.761 Å / Mean I/σ(I) obs: 0.56 / Num. unique obs: 3808 / CC_1/2: 0.171 / CC star: 0.541

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Processing

Software

Name	Version	Classification
PHENIX	1.19.1_4122	refinement
XDS		data reduction
Aimless		data scaling
AutoSol		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2317	2157	5.01 %
R_work	0.194	40895	-
obs	0.1958	43052	97.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 46.29 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→41.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2571	0	0	139	2710

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0087	2629
X-RAY DIFFRACTION	f_angle_d	1.0924	3562
X-RAY DIFFRACTION	f_chiral_restr	0.0616	395
X-RAY DIFFRACTION	f_plane_restr	0.0106	470
X-RAY DIFFRACTION	f_dihedral_angle_d	5.773	355

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7-1.74	0.5156	110	0.4849	2058	X-RAY DIFFRACTION	75.86
1.74-1.78	0.3964	138	0.3975	2580	X-RAY DIFFRACTION	93.79
1.78-1.83	0.3573	145	0.3269	2759	X-RAY DIFFRACTION	99.97
1.83-1.89	0.3147	144	0.2901	2747	X-RAY DIFFRACTION	99.93
1.89-1.95	0.3364	143	0.2774	2722	X-RAY DIFFRACTION	99.97
1.95-2.02	0.2603	145	0.2435	2765	X-RAY DIFFRACTION	99.76
2.02-2.1	0.2652	145	0.2127	2750	X-RAY DIFFRACTION	99.9
2.1-2.19	0.2631	146	0.1938	2764	X-RAY DIFFRACTION	99.97
2.19-2.31	0.2555	145	0.1935	2752	X-RAY DIFFRACTION	99.83
2.31-2.45	0.2482	147	0.1892	2781	X-RAY DIFFRACTION	99.93
2.45-2.64	0.2453	145	0.2083	2763	X-RAY DIFFRACTION	99.93
2.64-2.91	0.2566	148	0.1958	2805	X-RAY DIFFRACTION	99.97
2.91-3.33	0.2165	148	0.1923	2799	X-RAY DIFFRACTION	100
3.33-4.19	0.1963	151	0.1608	2854	X-RAY DIFFRACTION	99.97
4.19-41.68	0.1956	157	0.1723	2996	X-RAY DIFFRACTION	99.87

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.85438061649	1.86417818723	-0.613305006883	2.73192847923	2.5039199318	7.15826925412	-0.000712059909769	0.118127409759	-0.0597231204008	-0.16930456493	0.213364505729	-0.476390502071	0.0151419579755	0.447583352564	-0.243999642259	0.276125306209	0.0664988267047	0.0289302665778	0.268594824013	-0.0176361635593	0.410999877337	35.1457046461	30.8271539142	58.9001037448
2	2.15003677031	0.0967836364861	0.0189732443874	1.82046280451	-1.00570448226	4.84658559788	0.0679489219063	0.064954664165	-0.214227231299	-0.175319577566	0.0470912162689	-0.0180460631487	0.518654365984	0.0790683951724	-0.106496316864	0.32246439075	0.0344691064621	-0.0378282427817	0.216064926909	-0.0272783445234	0.403298084785	32.9967347237	22.3668172808	64.1840091596
3	2.48102399922	0.198548567691	0.822507112476	8.94223171728	-2.81048265361	5.1992144607	-0.0249262582825	0.144263716669	0.180176361734	-0.87986653627	0.0482776000385	0.136445813111	0.122439745896	-0.29105202622	-0.0025794571238	0.309450519891	-0.00632334145447	-0.0530624703964	0.307229433453	0.00193629212257	0.310365373108	24.4891759961	45.7973580217	43.9958664123
4	6.74145615361	2.16317998571	-1.97543637368	4.07100380456	-4.63602489897	7.67196198756	0.353456795179	0.442135245287	0.272733812026	-0.748060358459	-0.328335565175	0.023813289543	-0.232616883201	0.451608674287	-0.00103121770419	0.516100062365	0.0534209218621	0.0710225930667	0.321438451423	0.00800763790511	0.404919511527	27.5823936238	47.5347236665	42.1470024392
5	2.90267049236	-3.90579407961	2.91752043977	6.75545633807	-3.66891186125	3.89040984238	0.407148241081	0.144093249186	-0.922232290135	-1.3314144388	0.358395202825	2.27781943528	0.356644067348	-0.759631878272	-0.630952176888	0.62041976424	-0.00709632390862	-0.313060492697	0.485961524069	0.0662843325489	0.746627846414	16.8634893958	40.9710621784	40.4765081852
6	5.92809910599	-5.74637713051	6.60400478059	5.70256778456	-6.52970156615	7.45869774211	0.336706474039	0.596239311833	0.245412737783	-0.642084845359	-0.577493729659	-0.226750105281	0.437237542103	0.483384330344	0.324154998345	0.768578453665	0.179185526449	0.230394221067	0.509340714532	0.0539903120033	0.669539230127	38.2223072298	31.2792046941	41.7269104927
7	2.10888583647	1.19454604282	-0.353031146581	3.33106900758	-1.04443078388	3.84590168357	0.101272033759	-0.364773884864	0.0730132259708	1.89489154523	0.427280849281	-0.722988846203	-0.489967009347	-0.0938873079938	-0.473481303468	0.609214170799	-0.0824715734905	-0.061317801648	0.31964745581	-0.00508039189118	0.439741802257	26.8961884963	34.1411907852	85.0251806111
8	3.38366203986	0.066095701776	-1.1250775958	6.80906056985	-0.907115884467	2.58510945512	0.296694281501	-0.408913035988	-0.263932305332	0.955178522998	-0.285920130019	-0.613562439318	0.0393854548405	0.038319096234	-0.0105326199997	0.39124903329	-0.0572160013244	-0.13100385666	0.272772799248	0.0487656540977	0.353700248412	25.0604430917	16.8033413154	84.6728104512
9	2.58489055868	-1.29447312879	0.847428290491	2.59039257616	0.52376045831	4.60682113188	0.188451083611	-0.814174357217	-0.689997188834	0.464055782432	-0.882839758506	0.357445913629	1.31485450408	-0.424023947017	0.215448530531	1.37525109159	-0.197551249065	-0.40460112948	0.549334360744	0.141874283665	0.746850545067	30.5566546713	10.9605086577	98.6252551627
10	3.12806780324	2.86186180441	-0.469564217899	8.87846847962	-5.02829971451	7.44792380103	0.551673437943	0.0118890684157	0.145588807174	1.07353250245	-0.343304152326	0.238721016378	-0.00579685376329	-0.0176840484824	-0.266748970033	0.416733251527	-0.0528501384043	-0.00406697444445	0.212062199284	-0.0356903237829	0.307682794127	21.2372478159	24.6666294124	84.2234849431
11	5.40259835259	2.56233238735	2.03763858728	2.28786930926	2.39037601029	5.12168945311	0.71516809296	-0.0853888940806	0.552665316824	2.11913037584	-0.579978811702	0.971036557722	-0.000974764087146	-0.105675195296	-0.152247294439	0.718931735711	-0.129454441222	0.114401081349	0.380532988519	-0.0245823875525	0.459886726052	16.7676409037	19.0414737579	90.6047929365
12	7.36971473913	6.90158197463	-5.88663505663	8.84560422562	-6.33829954416	4.97589581904	-0.0913909934967	0.367957115499	0.174910252853	-0.259944648732	0.332072694944	0.0178002977663	-0.187313881001	-0.139166519423	-0.142529003035	0.205140552506	-0.00437616701165	-0.0117976088492	0.238797928708	-0.0164576345988	0.379095606756	35.7636721627	50.6456827089	62.2242812124
13	2.84912783155	0.646883214899	1.17828108384	3.90552567408	5.07304120999	8.52953007201	0.206300152755	-0.131778638375	-0.134459432673	0.341490868016	0.0900993069053	-0.314419167643	0.64108112026	0.103366746227	-0.308012362635	0.263608930185	0.000242789696585	-0.0289871620784	0.210701873476	0.0135138941896	0.342712987441	32.7900773397	37.8981020531	72.1668948668
14	2.82134639687	0.0963578691976	1.27549638575	1.71756203832	-0.342179376855	6.95499754803	-0.02561482244	0.198073795774	0.00514634252569	-0.0101584107967	-0.00443889796498	0.00426116800114	-0.120979671719	0.0546988451264	0.0199553553146	0.224504973893	0.00528966442771	-0.00391578454105	0.209602676013	-0.0141844680016	0.391680537892	31.4627519886	44.9603806644	62.9138185244
15	2.33073376641	-1.7503843481	2.04214327299	4.47183326838	-5.6056565998	6.90236209819	0.00895121485446	-0.0767702571545	-0.247967733732	0.540685623356	0.232819032388	0.523972069128	-0.213636282117	-0.594540085913	-0.394394399713	0.357295503093	0.0365524641699	0.0716435648272	0.316211417083	-0.0336144269112	0.418654277207	21.436905158	42.399713162	76.1950999308
16	3.53177864504	2.86538021992	-3.08099821723	2.49634210242	-2.56461082554	2.75671694846	0.387706962212	-0.205330181152	2.29589937341	0.166807518717	0.53920284554	0.672429133429	-0.424309888553	0.156444355568	-1.00307959281	0.35490293256	0.0197767571648	0.0537014755315	0.336828062763	0.00835111410685	0.699997951098	29.9389249538	53.4536280768	66.1973434809
17	0.136962944861	0.735968537315	-0.907412863394	4.51569476275	-5.56489636546	6.84076895218	-0.475743977152	0.201478993976	-0.202482622844	2.41164428345	0.262272846879	-0.840212079374	-2.28376238556	-1.2731704792	0.301850096625	0.781770645341	0.154672535229	-0.12979188502	0.642025890692	0.0298576118927	0.707050164808	46.7075021954	24.5181183615	72.3465208334
18	6.0297729223	-3.17864198486	4.22815200823	7.54268286946	-4.55167320514	4.14115936744	0.145755139836	0.428795153558	-0.252354234556	-0.378027661022	-0.321894867003	-0.465554810289	0.862072822762	1.60014745621	0.0730980247592	0.424029200289	0.109856136459	-0.0197168306312	0.307695250197	-0.05327476409	0.450647372679	39.1743543276	18.969305614	67.5746062114

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 209 through 223 )	B	B	209 - 223	16 - 30
2	2	chain 'B' and (resid 224 through 274 )	B	B	224 - 274	31 - 81
3	3	chain 'C' and (resid 7 through 36 )	C	C	7 - 36	1 - 30
4	4	chain 'C' and (resid 37 through 62 )	C	C	37 - 62	31 - 56
5	5	chain 'C' and (resid 63 through 89 )	C	C	63 - 89	57 - 83
6	6	chain 'C' and (resid 90 through 99 )	C	C	90 - 99	84 - 93
7	7	chain 'D' and (resid 8 through 13 )	D	D	8 - 13	1 - 6
8	8	chain 'D' and (resid 14 through 44 )	D	D	14 - 44	7 - 37
9	9	chain 'D' and (resid 45 through 52 )	D	D	45 - 52	38 - 45
10	10	chain 'D' and (resid 53 through 72 )	D	D	53 - 72	46 - 65
11	11	chain 'D' and (resid 73 through 91 )	D	D	73 - 91	66 - 84
12	12	chain 'A' and (resid 198 through 208 )	A	A	198 - 208	1 - 11
13	13	chain 'A' and (resid 209 through 223 )	A	A	209 - 223	12 - 26
14	14	chain 'A' and (resid 224 through 256 )	A	A	224 - 256	27 - 59
15	15	chain 'A' and (resid 257 through 267 )	A	A	257 - 267	60 - 70
16	16	chain 'A' and (resid 268 through 274 )	A	A	268 - 274	71 - 77
17	17	chain 'B' and (resid 194 through 200 )	B	B	194 - 200	1 - 7
18	18	chain 'B' and (resid 201 through 208 )	B	B	201 - 208	8 - 15

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