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- PDB-7d1l: complex structure of two RRM domains -

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Basic information

Entry
Database: PDB / ID: 7d1l
Titlecomplex structure of two RRM domains
Components
  • Embryonic developmental protein tofu-6
  • Uncharacterized protein
KeywordsPROTEIN BINDING / RRM / protein complex / RNA
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
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
Protein pid-3 / Embryonic developmental protein tofu-6
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsWang, X. / Liao, S. / Xu, C.
CitationJournal: Nat Commun / Year: 2021
Title: Molecular basis for PICS-mediated piRNA biogenesis and cell division.
Authors: Wang, X. / Zeng, C. / Liao, S. / Zhu, Z. / Zhang, J. / Tu, X. / Yao, X. / Feng, X. / Guang, S. / Xu, C.
History
DepositionSep 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Embryonic developmental protein tofu-6
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)41,5704
Polymers41,5704
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-22 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.686, 86.908, 92.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 10761.389 Da / Num. of mol.: 2 / Fragment: RRM1 domain / Mutation: LEU23MSE
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q09293
#2: Protein Uncharacterized protein


Mass: 10023.728 Da / Num. of mol.: 2 / Fragment: RRM2 domain / Mutation: ILE233MSE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: pid-3, CELE_Y23H5A.3, Y23H5A.3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O76616
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2% v/v 1, 4-Dioxane 0.1M Tris pH 8.0 15% w/v PEG3350 0.01 M Nickel(II) Chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 58993 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.143 / Net I/σ(I): 19.2
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 1.075 / Num. unique obs: 3258 / CC1/2: 0.722

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→27.653 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.81 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2247 3627 6.15 %
Rwork0.1843 55366 -
obs0.1868 58993 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.36 Å2 / Biso mean: 25.6598 Å2 / Biso min: 8.51 Å2
Refinement stepCycle: final / Resolution: 1.95→27.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 0 317 2874
Biso mean---35.37 -
Num. residues----328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9502-1.97590.27461080.2656140863
1.9759-2.0030.24941000.2421162773
2.003-2.03160.26491040.2354170275
2.0316-2.06190.22631320.2341183982
2.0619-2.09410.29361230.2152196286
2.0941-2.12840.27491430.2083201692
2.1284-2.16510.28731240.203217296
2.1651-2.20450.23561530.2054223199
2.2045-2.24680.24641320.19922229100
2.2468-2.29270.21251410.19922284100
2.2927-2.34250.21741600.20022214100
2.3425-2.3970.27951440.2032266100
2.397-2.45690.2911370.20482225100
2.4569-2.52330.23621470.19262256100
2.5233-2.59750.27891530.19942240100
2.5975-2.68120.26691440.18942248100
2.6812-2.7770.21541530.18362250100
2.777-2.8880.20711340.18252292100
2.888-3.01930.22311440.17412213100
3.0193-3.17830.27421570.18112241100
3.1783-3.37710.18771380.17472263100
3.3771-3.63730.17441460.15872269100
3.6373-4.00240.22091600.14822216100
4.0024-4.57930.18721490.14542239100
4.5793-5.76080.1851470.17312251100
5.7608-27.6530.22271540.2105221399
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)
11.0867-0.099-0.62380.6470.28991.7438-0.0183-0.10230.02870.07370.0523-0.0742-0.00730.2065-0.00020.16910.0255-0.01070.17660.00630.142625.486821.67128.0925
21.85990.2905-0.23871.68490.38161.2395-0.04910.0906-0.2683-0.16570.0374-0.05360.044-0.01410.00030.1991-0.00660.02190.13-0.00280.1638-6.1229-6.43011.708
31.07280.0990.27620.4830.43150.5598-0.13860.0821-0.14-0.02360.1192-0.0811-0.0020.1047-0.03040.12620.01320.04540.14160.00040.136421.683312.38096.6568
40.80620.37260.26770.47790.40610.3994-0.1031-0.06440.1141-0.0535-0.01020.08980.06080.0235-0.01930.10860.03010.00380.0994-0.01250.1109-2.046215.58839.7286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 9 through 92)A9 - 92
2X-RAY DIFFRACTION2(chain 'B' and resid 8 through 92)B8 - 92
3X-RAY DIFFRACTION3(chain 'C' and resid 200 through 282)C200 - 282
4X-RAY DIFFRACTION4(chain 'D' and resid 200 through 282)D200 - 282

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