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- PDB-7qrx: Crystal structure of NHL domain of TRIM71 -

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Basic information

Entry
Database: PDB / ID: 7qrx
TitleCrystal structure of NHL domain of TRIM71
ComponentsE3 ubiquitin-protein ligase TRIM71
KeywordsLIGASE / E3 / TRIM / TRIM71 / NHL domain
Function / homology
Function and homology information


regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / miRNA metabolic process / 3'-UTR-mediated mRNA destabilization / regulation of neural precursor cell proliferation / miRNA-mediated gene silencing by inhibition of translation / miRNA processing / neural tube development / miRNA binding / post-transcriptional regulation of gene expression ...regulation of miRNA-mediated gene silencing / positive regulation of miRNA-mediated gene silencing / miRNA metabolic process / 3'-UTR-mediated mRNA destabilization / regulation of neural precursor cell proliferation / 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 / Antigen processing: Ubiquitination & Proteasome degradation / 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 ...: / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iucrj / Year: 2022
Title: Comparative structural analyses of the NHL domains from the human E3 ligase TRIM-NHL family.
Authors: Chaikuad, A. / Zhubi, R. / Tredup, C. / Knapp, S.
History
DepositionJan 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: E3 ubiquitin-protein ligase TRIM71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,62820
Polymers61,5112
Non-polymers1,11718
Water2,630146
1
A: E3 ubiquitin-protein ligase TRIM71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,37611
Polymers30,7561
Non-polymers62110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase TRIM71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2529
Polymers30,7561
Non-polymers4978
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.750, 78.674, 92.852
Angle α, β, γ (deg.)90.000, 100.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 590 - 868 / Label seq-ID: 1 - 279

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 30755.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM71, LIN41 / Plasmid: pSUMO-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: Q2Q1W2, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.03 Å3/Da / Density % sol: 39.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 8.5, 0.2M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.2→45.71 Å / Num. obs: 25069 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.059 / Rrim(I) all: 0.156 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.287.10.8172.124500.8610.3520.95299.9
8.52-45.716.90.054530.9990.0210.05499.5

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6fql

6fql


Resolution: 2.2→45.71 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 18.029 / SU ML: 0.221 / SU R Cruickshank DPI: 0.4682 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2716 1181 4.7 %RANDOM
Rwork0.232 ---
obs0.2338 23870 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.25 Å2 / Biso mean: 35.363 Å2 / Biso min: 13.57 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20 Å2-0.47 Å2
2---0.22 Å20 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 2.2→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 72 146 4560
Biso mean--47.21 34.87 -
Num. residues----558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134510
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154204
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.6416046
X-RAY DIFFRACTIONr_angle_other_deg1.0911.5879622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0585558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.5321.471272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90415704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2361538
X-RAY DIFFRACTIONr_chiral_restr0.0420.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025273
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021179
Refine LS restraints NCS

Ens-ID: 1 / Number: 9255 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 83 -
Rwork0.301 1759 -
all-1842 -
obs--99.89 %
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)
12.166-0.18830.71313.77170.14543.10750.1038-0.0426-0.0350.1747-0.02650.13160.1888-0.0767-0.07730.0218-0.0011-0.00040.059-0.01280.01031.02794.629920.3727
24.50360.531-0.62155.4832-0.1494.7404-0.04320.2649-0.4188-0.59330.04390.23070.3606-0.0245-0.00080.18070.0059-0.04050.1345-0.08440.09050.0579-6.10633.7818
32.8133.043-0.00195.57930.24024.75150.00380.33240.3056-0.72070.08240.2227-0.1332-0.0306-0.08620.23380.07260.02970.13190.05540.0528-0.611.52073.5526
42.79020.3730.87623.78770.27972.73760.05420.03270.14880.0928-0.0516-0.2136-0.11770.0264-0.00260.0146-0.0158-0.00250.05350.01320.02441.9929.08950.5668
50.8764-0.41810.14125.5103-0.40575.84920.0754-0.1018-0.49020.0913-0.0283-0.00140.5399-0.1345-0.04710.0591-0.027-0.04580.14740.05780.28460.9363-8.719757.1536
62.70.270.01675.2951-1.68453.32290.0083-0.599-0.16991.02110.0907-0.4583-0.04460.0278-0.0990.2910.0032-0.08770.2899-0.00030.12264.53442.985369.575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A590 - 738
2X-RAY DIFFRACTION2A739 - 831
3X-RAY DIFFRACTION3A832 - 868
4X-RAY DIFFRACTION4B590 - 700
5X-RAY DIFFRACTION5B701 - 775
6X-RAY DIFFRACTION6B776 - 868

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