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- PDB-8j72: Crystal structure of mammalian Trim71 in complex with lncRNA Trincr1 -

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Basic information

Entry
Database: PDB / ID: 8j72
TitleCrystal structure of mammalian Trim71 in complex with lncRNA Trincr1
Components
  • E3 ubiquitin-protein ligase TRIM71
  • lncRNA Trincr1
KeywordsRNA BINDING PROTEIN / RNA / Trim71 / Complex
Function / homology
Function and homology information


regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / 3'-UTR-mediated mRNA destabilization / regulation of neural precursor cell proliferation / Antigen processing: Ubiquitination & Proteasome degradation / regulation of protein metabolic process / miRNA-mediated gene silencing by inhibition of translation / miRNA processing / neural tube development / miRNA binding ...regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / 3'-UTR-mediated mRNA destabilization / regulation of neural precursor cell proliferation / Antigen processing: Ubiquitination & Proteasome degradation / regulation of protein metabolic process / miRNA-mediated gene silencing by inhibition of translation / miRNA processing / neural tube development / miRNA binding / post-transcriptional regulation of gene expression / : / fibroblast growth factor receptor signaling pathway / protein autoubiquitination / translation repressor activity / stem cell proliferation / neural tube closure / 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 / negative regulation of translation / 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. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsShi, F.D. / Zhang, K. / Che, S.Y. / Zhi, S.X. / Yang, N.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508902 China
Ministry of Science and Technology (MoST, China)2018YFA0107004 China
National Natural Science Foundation of China (NSFC)32170549 China
CitationJournal: Sci Bull (Beijing) / Year: 2024
Title: Molecular mechanism governing RNA-binding property of mammalian TRIM71 protein.
Authors: Shi, F. / Zhang, K. / Cheng, Q. / Che, S. / Zhi, S. / Yu, Z. / Liu, F. / Duan, F. / Wang, Y. / Yang, N.
History
DepositionApr 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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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
C: lncRNA Trincr1


Theoretical massNumber of molelcules
Total (without water)65,2883
Polymers65,2883
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-5 kcal/mol
Surface area22460 Å2
Unit cell
Length a, b, c (Å)45.529, 51.450, 73.154
Angle α, β, γ (deg.)77.850, 75.870, 77.640
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein E3 ubiquitin-protein ligase TRIM71 / Protein lin-41 homolog / mLin41 / RING-type E3 ubiquitin transferase TRIM71 / Tripartite motif- ...Protein lin-41 homolog / mLin41 / RING-type E3 ubiquitin transferase TRIM71 / Tripartite motif-containing protein 71


Mass: 30867.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trim71, Gm1127, Lin41 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q1PSW8, RING-type E3 ubiquitin transferase
#2: RNA chain lncRNA Trincr1


Mass: 3552.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Ammonium tartrate dibasic pH7.0,12% PEG 3350 (w/v)

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2019
RadiationMonochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.16→40 Å / Num. obs: 10186 / % possible obs: 98.1 % / Redundancy: 3.8 % / CC1/2: 0.988 / Net I/σ(I): 10.14
Reflection shellResolution: 3.16→3.26 Å / Num. unique obs: 492 / CC1/2: 0.908

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FPT

6fpt


Resolution: 3.16→37.58 Å / Cross valid method: THROUGHOUT
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2814 492 -
Rwork0.2146 --
obs-9733 91.95 %
Displacement parametersBiso mean: 48.83 Å2
Refinement stepCycle: LAST / Resolution: 3.16→37.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4301 195 0 0 4496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00434624
X-RAY DIFFRACTIONf_angle_d0.88056274
X-RAY DIFFRACTIONf_chiral_restr0.0596646
X-RAY DIFFRACTIONf_plane_restr0.0049817
X-RAY DIFFRACTIONf_dihedral_angle_d17.46271702
LS refinement shellResolution: 3.16→3.48 Å /
Rfactor% reflection
Rfree0.3429 -
Rwork0.275 -
obs-73 %
Refinement TLS params.Method: refined / Origin x: 4.0614 Å / Origin y: 25.2579 Å / Origin z: 25.1139 Å
111213212223313233
T0.3804 Å2-0.0186 Å20.0005 Å2-0.3566 Å20.034 Å2--0.372 Å2
L0.611 °2-0.2029 °20.0359 °2-0.4585 °20.2697 °2--0.3063 °2
S-0.0415 Å °-0.01 Å °-0.0208 Å °0.0267 Å °0.0062 Å °-0.0066 Å °-0.0296 Å °-0.0312 Å °0.0087 Å °
Refinement TLS groupSelection details: all

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