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- PDB-7d2y: complex of two RRM domains -

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Basic information

Entry
Database: PDB / ID: 7d2y
Titlecomplex of two RRM domains
Components
  • Embryonic developmental protein tofu-6
  • RRM2
KeywordsPROTEIN BINDING / RRM domain
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 / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsWang, X. / Liao, S. / Xu, C.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
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 17, 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: RRM2
D: RRM2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1586
Polymers38,9664
Non-polymers1922
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-62 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.961, 116.961, 140.168
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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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: 10411.639 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q09293
#2: Protein RRM2


Mass: 9071.353 Da / Num. of mol.: 2
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris pH 8.5, 2.0M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 27391 / % possible obs: 100 % / Redundancy: 37.7 % / CC1/2: 1 / Net I/σ(I): 0.039
Reflection shellResolution: 2.68→2.78 Å / Rmerge(I) obs: 1.161 / Num. unique obs: 1593 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D1L

7d1l


Resolution: 2.68→23.361 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 2738 10 %
Rwork0.1947 24653 -
obs0.1989 27391 91.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.87 Å2 / Biso mean: 46.6363 Å2 / Biso min: 13.52 Å2
Refinement stepCycle: final / Resolution: 2.68→23.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2561 0 10 38 2609
Biso mean--77.56 33.9 -
Num. residues----330
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6804-2.72660.273880.292578157
2.7266-2.77610.3387890.289380860
2.7761-2.82940.32311040.280388466
2.8294-2.8870.37481130.2414102675
2.887-2.94970.30131340.2319115785
2.9497-3.01820.26141390.2308123593
3.0182-3.09350.26971510.21931372100
3.0935-3.17690.26541490.22361336100
3.1769-3.27020.24671460.21421360100
3.2702-3.37540.24981510.22951363100
3.3754-3.49570.25431430.20381342100
3.4957-3.63520.22591520.18811354100
3.6352-3.79990.24551500.18561367100
3.7999-3.99930.24441530.17121336100
3.9993-4.24850.20391440.16821370100
4.2485-4.57430.20711510.16391340100
4.5743-5.03050.23011510.16811358100
5.0305-5.74890.22541450.1944134099
5.7489-7.20750.21911450.1957127594
7.2075-23.360.16641400.1638124992
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)
11.14280.594-0.00741.1574-0.25141.5148-0.1350.02380.39410.1958-0.0640.0323-0.5060.37520.08070.683-0.2884-0.17310.34470.01110.457846.4333-24.934523.479
20.4230.1024-0.37160.0302-0.01821.2294-0.1750.78110.3781-0.36820.13530.2085-0.2362-0.14430.08280.4868-0.2405-0.22271.00110.3280.540522.082-35.6659-18.2384
31.80580.20420.00251.3044-0.26952.1589-0.13940.16850.39120.13790.01650.2858-0.3355-0.06010.110.1475-0.0598-0.01770.2465-0.00570.278427.9511-37.08913.645
40.9210.2588-0.25440.5106-0.33431.0737-0.13820.46640.1861-0.16710.10380.0235-0.16590.21170.11330.195-0.28440.00550.69450.06160.237141.3386-40.0828-5.864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 8 through 92)A8 - 94
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 91)B7 - 93
3X-RAY DIFFRACTION3(chain 'C' and resid 200 through 281)C7 - 88
4X-RAY DIFFRACTION4(chain 'D' and resid 201 through 281)D8 - 88

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