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- PDB-6fq3: Crystal structure of Danio rerio Lin41 filamin-NHL domains in com... -

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Basic information

Entry
Database: PDB / ID: 6fq3
TitleCrystal structure of Danio rerio Lin41 filamin-NHL domains in complex with lin-29A 5'UTR 13mer RNA
Components
  • E3 ubiquitin-protein ligase TRIM71
  • RNA (5'-R(*GP*GP*AP*GP*UP*CP*CP*AP*AP*CP*UP*CP*C)-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 / protein autoubiquitination / fibroblast growth factor receptor signaling pathway / 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 / protein autoubiquitination / fibroblast growth factor receptor signaling pathway / 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 / B-Box-type 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: 1.901 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 13, 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(*GP*GP*AP*GP*UP*CP*CP*AP*AP*CP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,02510
Polymers48,7412
Non-polymers2848
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-67 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.850, 101.850, 109.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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 of Lin41 encompassing filamin-NHL domains (residues 435-824)
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: trim71, lin41 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: E7FAM5, RING-type E3 ubiquitin transferase
#2: RNA chain RNA (5'-R(*GP*GP*AP*GP*UP*CP*CP*AP*AP*CP*UP*CP*C)-3')


Mass: 4116.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fragment of lin-29a 5'UTR / Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: synthetic construct (others)
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% PEG 8000 20% ethylene glycol 0.1M carboxylic acids 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 51941 / % possible obs: 99.4 % / Redundancy: 7.7 % / Biso Wilson estimate: 56.1 Å2 / CC1/2: 0.99 / Rsym value: 0.042 / Net I/σ(I): 20.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 0.81 / Num. unique obs: 3516 / CC1/2: 0.381 / Rsym value: 2.172 / % possible all: 92.1

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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: 1.901→46.637 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.04
RfactorNum. reflection% reflection
Rfree0.1804 2596 5 %
Rwork0.1581 --
obs0.1592 51933 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.4 Å2
Refinement stepCycle: LAST / Resolution: 1.901→46.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2994 272 8 237 3511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073402
X-RAY DIFFRACTIONf_angle_d0.7924658
X-RAY DIFFRACTIONf_dihedral_angle_d11.6621959
X-RAY DIFFRACTIONf_chiral_restr0.062494
X-RAY DIFFRACTIONf_plane_restr0.006584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9013-1.93580.43711200.41982291X-RAY DIFFRACTION89
1.9358-1.97310.32991370.32052594X-RAY DIFFRACTION100
1.9731-2.01340.30041350.26972563X-RAY DIFFRACTION100
2.0134-2.05710.27971360.2442596X-RAY DIFFRACTION100
2.0571-2.1050.24311350.21612585X-RAY DIFFRACTION100
2.105-2.15760.23991360.20542574X-RAY DIFFRACTION100
2.1576-2.2160.2361360.19162592X-RAY DIFFRACTION100
2.216-2.28120.21811360.18792586X-RAY DIFFRACTION100
2.2812-2.35480.221370.17652598X-RAY DIFFRACTION100
2.3548-2.4390.21871370.17932590X-RAY DIFFRACTION100
2.439-2.53660.19191370.17532607X-RAY DIFFRACTION100
2.5366-2.6520.22981350.17772576X-RAY DIFFRACTION100
2.652-2.79180.20491380.18162617X-RAY DIFFRACTION100
2.7918-2.96670.20851380.17832624X-RAY DIFFRACTION100
2.9667-3.19570.2061390.17232636X-RAY DIFFRACTION100
3.1957-3.51730.1731380.16082624X-RAY DIFFRACTION100
3.5173-4.0260.16941390.15072637X-RAY DIFFRACTION100
4.026-5.07130.13131400.1122665X-RAY DIFFRACTION100
5.0713-46.65070.15661470.1442782X-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)
15.0373-0.81860.43524.9040.2864.6982-0.0245-0.28550.28330.15340.0773-0.5480.01580.4425-0.04580.2928-0.0154-0.05050.5176-0.07160.5657-116.618286.8013225.8476
22.21940.5313-0.18062.4824-0.46972.42280.00030.4290.047-0.72030.08450.27490.1012-0.0907-0.07860.52240.0581-0.07880.45010.0360.3911-82.0549272.3873233.0776
36.0858-1.0512.6153.0757-2.04936.61490.30150.4834-0.355-0.0959-0.2606-0.1633-0.10710.9225-0.00260.50810.08790.08970.55760.06540.5016-62.378263.3322244.6277
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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