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- PDB-6fpt: Crystal structure of Danio rerio Lin41 filamin-NHL domains -

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Basic information

Entry
Database: PDB / ID: 6fpt
TitleCrystal structure of Danio rerio Lin41 filamin-NHL domains
ComponentsE3 ubiquitin-protein ligase TRIM71
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 / neural tube development / miRNA binding / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / stem cell proliferation / P-body / RING-type E3 ubiquitin transferase ...Antigen processing: Ubiquitination & Proteasome degradation / regulation of neural precursor cell proliferation / miRNA-mediated gene silencing by inhibition of translation / neural tube development / miRNA binding / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / stem cell proliferation / P-body / RING-type E3 ubiquitin transferase / G1/S transition of mitotic cell cycle / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / 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
E3 ubiquitin-protein ligase TRIM71
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 12, 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

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM71
B: E3 ubiquitin-protein ligase TRIM71


Theoretical massNumber of molelcules
Total (without water)89,2502
Polymers89,2502
Non-polymers00
Water3,873215
1
A: E3 ubiquitin-protein ligase TRIM71


Theoretical massNumber of molelcules
Total (without water)44,6251
Polymers44,6251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase TRIM71


Theoretical massNumber of molelcules
Total (without water)44,6251
Polymers44,6251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.800, 90.590, 131.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment encompassing the filamin-NHL domain (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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 8000 0.2 M magnesium chloride 0.1 M Tris pH 7.0 0.1 M trisodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.26 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 42647 / % possible obs: 91.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 45.33 Å2 / CC1/2: 0.987 / Rsym value: 0.124 / Net I/σ(I): 5.28
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 1.8 % / Num. unique obs: 3006 / CC1/2: 0.779 / Rsym value: 0.491 / % possible all: 86.8

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology models based on PDB IDs 4UMG and 1Q7F

4umg

1q7f


Resolution: 2.6→46.43 Å / Cor.coef. Fo:Fc: 0.9394 / Cor.coef. Fo:Fc free: 0.8825 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.329
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 1182 5 %RANDOM
Rwork0.1815 ---
obs0.1847 23630 95.35 %-
Displacement parametersBiso mean: 30.59 Å2
Baniso -1Baniso -2Baniso -3
1--3.2829 Å20 Å20 Å2
2---2.6882 Å20 Å2
3---5.9711 Å2
Refine analyzeLuzzati coordinate error obs: 0.309 Å
Refinement stepCycle: 1 / Resolution: 2.6→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6002 0 0 215 6217
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016150HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.28307HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2095SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes162HARMONIC2
X-RAY DIFFRACTIONt_gen_planes931HARMONIC5
X-RAY DIFFRACTIONt_it6150HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion19.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion737SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7047SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2855 137 5.01 %
Rwork0.2108 2599 -
all0.2144 2736 -
obs--95.35 %
Refinement TLS params.

L22: 0 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°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)
11.31710.264-0.14830.06980.1031-0.05270.2019-0.04240.00290.0162-0.050.04210.0580.0365-0.1546-0.00950.01130.2656-0.0012-0.184762.262685.5141284.261
20.747-0.2219-0.00210.04990.1977-0.0295-0.0683-0.0466-0.01330.03020.0431-0.01-0.0359-0.0006-0.1377-0.0085-0.01320.22030.0148-0.136769.341584.9568317.318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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