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- PDB-7xyy: TRIM E3 ubiquitin ligase WT -

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Basic information

Entry
Database: PDB / ID: 7xyy
TitleTRIM E3 ubiquitin ligase WT
ComponentsTripartite motif-containing protein 72
KeywordsMEMBRANE PROTEIN / TRIM / Tripartite motif / Ubiquitin ligase / Coiled coil / B-box / PRY-SPRY / LIGASE / METAL BINDING PROTEIN / TRIM72 / MG53
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 / sarcolemma / cytoplasmic vesicle membrane / protein homooligomerization / 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: 7.1 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
DepositionJun 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 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 / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,8796
Polymers105,6172
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Dimer, cross-linking, Dimer, Higher-order assembly on the liposome surface, gel filtration, Dimer, Higher-order assembly on the liposome surface, electron microscopy, Higher-order ...Evidence: SAXS, Dimer, cross-linking, Dimer, Higher-order assembly on the liposome surface, gel filtration, Dimer, Higher-order assembly on the liposome surface, electron microscopy, Higher-order assembly on the liposome surface
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-68 kcal/mol
Surface area51010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)367.044, 98.064, 103.203
Angle α, β, γ (deg.)90.000, 101.320, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 85 through 127 or resid 129...
d_2ens_1(chain "B" and (resid 85 through 127 or resid 129...

NCS oper: (Code: givenMatrix: (-0.999918096518, 8.77402917676E-5, -0.0127981466755), (0.000358888102215, -0.999391044431, -0.0348914246087), (-0.0127934145566, -0.0348931599821, 0.999309159335)Vector: ...NCS oper: (Code: given
Matrix: (-0.999918096518, 8.77402917676E-5, -0.0127981466755), (0.000358888102215, -0.999391044431, -0.0348914246087), (-0.0127934145566, -0.0348931599821, 0.999309159335)
Vector: -19.7374274341, -2.06452886595, -0.58843066582)

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Components

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


Mass: 52808.512 Da / Num. of mol.: 2
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.: 4 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.8 M NaCl, 8% (v/v) Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 7.1→50 Å / Num. obs: 5511 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 331.08 Å2 / CC1/2: 0.974 / CC star: 0.993 / Net I/σ(I): 10.1
Reflection shellResolution: 7.1→7.22 Å / Num. unique obs: 251 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XV2

7xv2


Resolution: 7.1→49.03 Å / SU ML: 1.2948 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.6623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3137 549 10.03 %
Rwork0.2694 4923 -
obs0.2742 5472 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 295.71 Å2
Refinement stepCycle: LAST / Resolution: 7.1→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 4 0 6036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00296160
X-RAY DIFFRACTIONf_angle_d0.77168334
X-RAY DIFFRACTIONf_chiral_restr0.0441916
X-RAY DIFFRACTIONf_plane_restr0.0051098
X-RAY DIFFRACTIONf_dihedral_angle_d5.8551832
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.12145693467 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.1-7.810.42521220.36271158X-RAY DIFFRACTION93.57
7.82-8.940.3931380.32481241X-RAY DIFFRACTION99.35
8.94-11.230.28541380.24641248X-RAY DIFFRACTION99.93
11.24-49.030.27441510.23761276X-RAY DIFFRACTION98.69
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)
16.062347344242.91341754459-3.59145452149.61020325098-8.6038596948.177783133121.5288059705-1.27069944507-0.723229351397-4.72926622562-3.709768259713.81249392174-0.76894741069-1.969435666621.997409927913.714256477830.4227601099840.3274553942662.60908620663-1.505680540685.08935009912-93.909424647623.254846674450.7882321212
23.03628573804-2.28819004512-1.038127455951.220607999312.079973014270.6766301677730.784393785612-2.13439144798-6.75990741215-0.5441013972270.3687526501671.06836534331-0.177761982608-0.0410279455509-1.131014201672.37780761788-0.342097353625-0.159221504573.009319592391.921480737963.66724499623-3.90854931102-7.9712947501549.5610454367
32.25435882791-4.122434620142.377932899818.51930430302-4.584160545272.37317346937-1.69763630052.301515365421.60832925617-1.91749687124-0.597845582067-2.518042488291.147814904810.2943410222721.40964182552.624087982211.32186428758-0.6367807405876.61758224996-0.08938054809591.281515346898.70813485224-6.0561051405833.6509593514
48.799288623994.12182323959-2.515145233064.95483448351-5.403261381886.181732822361.92585618296-2.01729659236-2.86555418454-3.88321040039-1.33086587570.2763752291290.01863565230750.995728990933-0.007586297259783.707486193550.231334305353-0.01430394428553.06112816293-1.638290748133.88833276749-19.6117643173-28.751390652518.4396597687
57.16310155434-0.129775340995-6.436788969491.80580788859-3.000347305971.979589087433.706793982093.54716355217-1.69430834436-4.96191018486-1.169786373420.532879078919-1.14374984847-6.54876073773-3.00287313144.565820457471.45934582326-0.2943676503223.886894375480.4172202745253.52818144381-23.4032287302-15.84694114966.12091997942
66.96289714918-2.82888476924-6.029903548276.88525426165-1.362657363037.606328207731.49302310209-1.05712259234-1.84363257987-0.028486793607-2.017538954331.60100196414-0.5047888062192.593160877520.0747401755412.8712957515-0.2456713863580.1417276232253.17920051288-1.407367686262.6711789004-15.9388189166-16.670020860517.5153833013
78.35090703684-2.08525209307-0.3343626506251.14847718324-1.28497302010.1530989464374.385529246980.100144193039-0.432400709766-1.11757969569-2.46950730688-0.429908083751-0.3227469497130.0980977150097-1.492957742272.582786590030.120622489712-0.6986854674653.74578802391-1.339408102283.228614834233.19124698384-2.8696516675549.6163894641
83.90288486126-4.59819176585-1.388117431638.704770002661.337630181380.5119576987480.4439640100673.43319434991-3.382090057860.999562006089-1.842424196241.90383177498-1.155022081561.29861940203-0.3014995972243.32615917474-0.501975691744-0.3845961142455.620234568140.007960939313030.652384777817-28.68925606892.7608692016133.0687262322
94.38725269959-3.658665303270.5991938691045.879975395313.852837974639.10011568181-1.44799396712-0.9335910114752.62706901243-0.7941349388410.759420432902-2.13602218704-1.08993330407-1.568356152450.652107625722.786569878140.0984751902871-0.304200440851.873088822750.1339448209852.284381381771.2852096065824.373371682316.4332696005
107.237818845784.362506913282.3793723231110.05689341992.324536459572.744093899991.86921761498-0.65029434626-0.04318719223810.812144810977-2.77658192587-0.3557928119480.0999966903085-0.804588162580.5136093677152.172282308370.363129943391-0.1010239402211.655899610070.09823167912591.62195329844-3.9348908186212.853981583814.9855837387
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 85 through 121 )AA85 - 1211 - 37
22chain 'A' and (resid 122 through 253 )AA122 - 25338 - 169
33chain 'A' and (resid 254 through 283 )AA254 - 283170 - 195
44chain 'A' and (resid 284 through 362 )AA284 - 362196 - 274
55chain 'A' and (resid 363 through 403 )AA363 - 403275 - 315
66chain 'A' and (resid 404 through 470 )AA404 - 470316 - 382
77chain 'B' and (resid 85 through 253 )BB85 - 2531 - 169
88chain 'B' and (resid 254 through 283 )BB254 - 283170 - 195
99chain 'B' and (resid 284 through 386 )BB284 - 386196 - 298
1010chain 'B' and (resid 387 through 470 )BB387 - 470299 - 382

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