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- PDB-7xv2: TRIM E3 ubiquitin ligase -

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Basic information

Entry
Database: PDB / ID: 7xv2
TitleTRIM E3 ubiquitin ligase
ComponentsTripartite motif-containing protein 72
KeywordsMEMBRANE PROTEIN / TRIM / Tripartite motif / Ubiquitin ligase / Coiled coil / B-box / PRY-SPRY / LIGASE / METAL BINDING PROTEIN
Function / homology
Function and homology information


muscle system process / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of myotube differentiation / vesicle budding from membrane / plasma membrane repair / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / muscle organ development / phosphatidylserine binding / exocytosis ...muscle system process / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of myotube differentiation / vesicle budding from membrane / plasma membrane repair / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / muscle organ development / phosphatidylserine binding / exocytosis / negative regulation of insulin receptor signaling pathway / cytoplasmic vesicle membrane / protein homooligomerization / sarcolemma / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. ...Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Tripartite motif-containing protein 72
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPark, S.H. / Song, H.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other government Korea, Republic Of
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Structure and activation of the RING E3 ubiquitin ligase TRIM72 on the membrane.
Authors: Si Hoon Park / Juhyun Han / Byung-Cheon Jeong / Ju Han Song / Se Hwan Jang / Hyeongseop Jeong / Bong Heon Kim / Young-Gyu Ko / Zee-Yong Park / Kyung Eun Lee / Jaekyung Hyun / Hyun Kyu Song /
Abstract: Defects in plasma membrane repair can lead to muscle and heart diseases in humans. Tripartite motif-containing protein (TRIM)72 (mitsugumin 53; MG53) has been determined to rapidly nucleate vesicles ...Defects in plasma membrane repair can lead to muscle and heart diseases in humans. Tripartite motif-containing protein (TRIM)72 (mitsugumin 53; MG53) has been determined to rapidly nucleate vesicles at the site of membrane damage, but the underlying molecular mechanisms remain poorly understood. Here we present the structure of Mus musculus TRIM72, a complete model of a TRIM E3 ubiquitin ligase. We demonstrated that the interaction between TRIM72 and phosphatidylserine-enriched membranes is necessary for its oligomeric assembly and ubiquitination activity. Using cryogenic electron tomography and subtomogram averaging, we elucidated a higher-order model of TRIM72 assembly on the phospholipid bilayer. Combining structural and biochemical techniques, we developed a working molecular model of TRIM72, providing insights into the regulation of RING-type E3 ligases through the cooperation of multiple domains in higher-order assemblies. Our findings establish a fundamental basis for the study of TRIM E3 ligases and have therapeutic implications for diseases associated with membrane repair.
History
DepositionMay 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tripartite motif-containing protein 72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3313
Polymers44,2011
Non-polymers1312
Water00
1
A: Tripartite motif-containing protein 72
hetero molecules

A: Tripartite motif-containing protein 72
hetero molecules


  • defined by author&software
  • Evidence: SAXS, Dimer, cross-linking, Dimer, Membrane bound oligomer, electron microscopy, Membrane bound oligomer in Negative-EM, Cryo-EM, Cryo-ET, gel filtration, Dimer, Membrane bound oligomer, ...Evidence: SAXS, Dimer, cross-linking, Dimer, Membrane bound oligomer, electron microscopy, Membrane bound oligomer in Negative-EM, Cryo-EM, Cryo-ET, gel filtration, Dimer, Membrane bound oligomer, homology, Dimer, mass spectrometry, Dimer in solution and oligomer on membrane surface by cross-link mass spectrometry
  • 88.7 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)88,6636
Polymers88,4012
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9840 Å2
ΔGint-84 kcal/mol
Surface area41820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.295, 110.171, 95.936
Angle α, β, γ (deg.)90.000, 100.801, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Tripartite motif-containing protein 72 / Mitsugumin-53 / Mg53


Mass: 44200.523 Da / Num. of mol.: 1 / Mutation: C144S,C242S,K279H,A283H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trim72, Mg53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1XH17
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris-HCl pH 8.5, 30% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 19188 / % possible obs: 97.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 80.36 Å2 / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.087 / Net I/σ(I): 27.3
Reflection shellResolution: 2.75→2.8 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 948 / CC1/2: 0.806 / CC star: 0.945 / % possible all: 98.9

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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: 3KB5

3kb5


Resolution: 2.75→27.41 Å / SU ML: 0.4255 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.2552
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 1900 10 %
Rwork0.2048 17094 -
obs0.2101 18994 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 115.04 Å2
Refinement stepCycle: LAST / Resolution: 2.75→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 2 0 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893088
X-RAY DIFFRACTIONf_angle_d1.11314179
X-RAY DIFFRACTIONf_chiral_restr0.0633458
X-RAY DIFFRACTIONf_plane_restr0.007551
X-RAY DIFFRACTIONf_dihedral_angle_d20.9532416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.38551330.34271199X-RAY DIFFRACTION97.23
2.82-2.890.43761360.3081209X-RAY DIFFRACTION97.46
2.9-2.980.35571350.30021228X-RAY DIFFRACTION97.5
2.98-3.080.42771340.33281203X-RAY DIFFRACTION98.02
3.08-3.190.37421380.29561239X-RAY DIFFRACTION98.22
3.19-3.310.32041390.26871250X-RAY DIFFRACTION98.79
3.31-3.460.33081370.24661237X-RAY DIFFRACTION99.35
3.46-3.650.28741380.23321239X-RAY DIFFRACTION99.35
3.65-3.870.25561380.20151239X-RAY DIFFRACTION99.35
3.87-4.170.22381380.18681237X-RAY DIFFRACTION99.06
4.17-4.590.211380.16071249X-RAY DIFFRACTION99
4.59-5.250.2131370.1551234X-RAY DIFFRACTION98.78
5.25-6.60.24541410.18921261X-RAY DIFFRACTION99.43
6.6-27.410.21661180.18181070X-RAY DIFFRACTION83.54
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)
18.041546240780.196620859604-5.334772575910.0738913314924-0.1300347514094.802600064950.4000456933061.026050557890.7052304516620.0143617401770.1333660182290.00981979787423-0.42937990658-0.91401779773-0.5331453821930.6848614706930.07094212077980.1373866758760.5462816117810.1456859398430.66845321835121.395265166917.302634139146.5929694913
21.86001557088-1.13899316715-1.992871148980.7898474799421.309861394682.19674400919-0.256828571766-0.0635302363811-0.6176496381770.0618092164271-0.2603155177610.425276428156-0.000209714246843-0.631283957190.5479909721140.7103936005860.08339193063260.2174781623090.7059213727960.1027801137870.94635460428211.45474805054.3016912641456.5706585644
34.422391184750.2861906247270.3845451482135.723305492432.835309606956.607564132020.1956088784340.612443192373-0.593844362058-1.108112153130.2778085409270.3712175627170.0598355816417-0.452086041238-0.3944625093310.946074002556-0.15452096168-0.2528323532880.582576763504-0.006955457810170.77479786625819.5756735447-14.913264364625.8874859709
46.99956367532-1.924577073931.728309533677.833054667660.8113761121449.139861079190.475695580245-0.2380242794290.9349326300490.326823806433-0.168916424466-0.7074500593630.1951836509890.787030280444-0.3416820168780.613020588251-0.116738753187-0.01610095932582.19861004527-0.1654979069081.09464802303104.7421526915.60200146595.77397328058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 119 through 251 )
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 284 )
3X-RAY DIFFRACTION3chain 'A' and (resid 285 through 470 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 118 )

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