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- PDB-6fql: Crystal structure of Danio rerio Lin41 filamin-NHL domains in com... -

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Basic information

Entry
Database: PDB / ID: 6fql
TitleCrystal structure of Danio rerio Lin41 filamin-NHL domains in complex with mab-10 3'UTR 13mer RNA
Components
  • E3 ubiquitin-protein ligase TRIM71
  • RNA (5'-R(*UP*GP*CP*AP*UP*UP*UP*AP*AP*UP*GP*CP*A)-3')
KeywordsRNA BINDING PROTEIN / post-transcriptional regulation
Function / homology
Function and homology information


Antigen processing: Ubiquitination & Proteasome degradation / regulation of neural precursor cell proliferation / miRNA-mediated gene silencing by inhibition of translation / miRNA binding / neural tube development / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / stem cell proliferation / P-body / G1/S transition of mitotic cell cycle ...Antigen processing: Ubiquitination & Proteasome degradation / regulation of neural precursor cell proliferation / miRNA-mediated gene silencing by inhibition of translation / miRNA binding / neural tube development / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / stem cell proliferation / P-body / G1/S transition of mitotic cell cycle / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / zinc ion binding
Similarity search - Function
: / NHL repeat profile. / NHL repeat / NHL repeat / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / B-box zinc finger ...: / NHL repeat profile. / NHL repeat / NHL repeat / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like fold
Similarity search - Domain/homology
RNA / RNA (> 10) / E3 ubiquitin-protein ligase TRIM71
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Caenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.349 Å
AuthorsKumari, P. / Aeschimann, F. / Gaidatzis, D. / Keusch, J.J. / Ghosh, P. / Neagu, A. / Pachulska-Wieczorek, K. / Bujnicki, J.M. / Gut, H. / Grosshans, H. / Ciosk, R.
CitationJournal: Nat Commun / Year: 2018
Title: Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.
Authors: Kumari, P. / Aeschimann, F. / Gaidatzis, D. / Keusch, J.J. / Ghosh, P. / Neagu, A. / Pachulska-Wieczorek, K. / Bujnicki, J.M. / Gut, H. / Grosshans, H. / Ciosk, R.
History
DepositionFeb 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM71
B: RNA (5'-R(*UP*GP*CP*AP*UP*UP*UP*AP*AP*UP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,01210
Polymers48,7282
Non-polymers2848
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Fluorescence polarization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-70 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.490, 101.490, 108.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-902-

CL

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM71 / Protein lin-41 homolog / RING-type E3 ubiquitin transferase TRIM71 / Tripartite motif-containing protein 71


Mass: 44624.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fragment: Lin41 filamin-NHL domains (residues 435-824)
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trim71, lin41 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): SF9
References: UniProt: E7FAM5, RING-type E3 ubiquitin transferase
#2: RNA chain RNA (5'-R(*UP*GP*CP*AP*UP*UP*UP*AP*AP*UP*GP*CP*A)-3')


Mass: 4103.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Fragment of C. elegans mab-10 3'UTR / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.32 Å3/Da / Density % sol: 62.99 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG 8000 20% ethylene glycol 0.1 M carboxylic acids 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.349→50 Å / Num. obs: 27367 / % possible obs: 99.4 % / Redundancy: 16.4 % / Biso Wilson estimate: 62.8 Å2 / CC1/2: 0.99 / Rsym value: 0.124 / Net I/σ(I): 16
Reflection shellResolution: 2.349→2.41 Å / Redundancy: 15.4 % / Num. unique obs: 1846 / CC1/2: 0.429 / Rsym value: 2.468 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FPT

6fpt


Resolution: 2.349→46.3 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.78
RfactorNum. reflection% reflection
Rfree0.2108 1368 5 %
Rwork0.1718 --
obs0.1739 27359 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67.1 Å2
Refinement stepCycle: LAST / Resolution: 2.349→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 271 8 92 3365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073389
X-RAY DIFFRACTIONf_angle_d0.8424639
X-RAY DIFFRACTIONf_dihedral_angle_d12.9481950
X-RAY DIFFRACTIONf_chiral_restr0.056493
X-RAY DIFFRACTIONf_plane_restr0.005581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3492-2.43310.32791280.29462430X-RAY DIFFRACTION94
2.4331-2.53050.30141370.26472590X-RAY DIFFRACTION100
2.5305-2.64570.31671330.23172549X-RAY DIFFRACTION100
2.6457-2.78510.24751360.21842595X-RAY DIFFRACTION100
2.7851-2.95960.24181370.21582595X-RAY DIFFRACTION100
2.9596-3.18810.2721360.20842592X-RAY DIFFRACTION100
3.1881-3.50880.25011380.19152612X-RAY DIFFRACTION100
3.5088-4.01630.24151380.16392628X-RAY DIFFRACTION100
4.0163-5.05910.14171390.12712643X-RAY DIFFRACTION100
5.0591-46.30870.17321460.15012757X-RAY DIFFRACTION100
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)
13.9822-0.4839-0.04734.7614-0.41774.1149-0.0205-0.2899-0.35760.12650.09820.5638-0.023-0.3891-0.09190.3557-0.00210.08120.56420.09690.6328166.9065-197.9677332.7507
22.01190.44670.08052.60130.35932.40740.06730.5098-0.0297-0.91910.0334-0.2868-0.13910.0098-0.10390.65270.07820.09020.4952-0.01830.4241132.395-183.3116339.7985
36.5495-0.4725-2.49243.36780.75676.91220.39280.29620.3561-0.1309-0.31160.57140.117-1.1334-0.08350.70460.0753-0.11630.7612-0.10430.6922112.8868-174.4037351.5375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 435 through 537 )
2X-RAY DIFFRACTION2chain 'A' and (resid 538 through 824 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 13 )

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