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- PDB-7xz2: TRIM E3 ubiquitin ligase -

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Basic information

Entry
Database: PDB / ID: 7xz2
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 / 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 / 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: 3.5 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
C: Tripartite motif-containing protein 72
D: Tripartite motif-containing protein 72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,85514
Polymers207,2014
Non-polymers65410
Water0
1
A: Tripartite motif-containing protein 72
B: Tripartite motif-containing protein 72
hetero molecules


  • defined by author
  • Evidence: SAXS, Dimer, electron microscopy, Higher-order assembly on the liposome, cross-linking, Dimer, Higher-order assembly on the liposome, gel filtration, Dimer, Higher-order assembly on the ...Evidence: SAXS, Dimer, electron microscopy, Higher-order assembly on the liposome, cross-linking, Dimer, Higher-order assembly on the liposome, gel filtration, Dimer, Higher-order assembly on the liposome, light scattering, Dimer
  • 104 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)103,9287
Polymers103,6012
Non-polymers3275
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tripartite motif-containing protein 72
D: Tripartite motif-containing protein 72
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9287
Polymers103,6012
Non-polymers3275
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.001, 326.949, 120.947
Angle α, β, γ (deg.)90.000, 90.890, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 85 through 117 or resid 119...
d_2ens_1(chain "B" and (resid 85 through 117 or resid 119...
d_3ens_1(chain "C" and (resid 85 through 117 or resid 119...

NCS oper:
IDCodeMatrixVector
1given(-0.513111226552, 0.452055982291, 0.729631590641), (0.441731114937, -0.589771766991, 0.676049469312), (0.735928319392, 0.669189548435, 0.102931321675)-73.1770916365, -0.848942952603, 49.0329696777
2given(-0.999844390085, -0.00420084190274, -0.0171332584047), (-0.00712015089913, 0.984706936195, 0.174073413423), (0.0161399835014, 0.17416831726, -0.98458361666)-77.3403027863, -6.40244357693, 63.8723923232

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Components

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


Mass: 51800.301 Da / Num. of mol.: 4 / Mutation: C55S, C144S, C241S, 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.: 10 / 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: 00 mM Na HEPES NaOH pH 7.5, 230 mM MgCl2, 100 mM CsCl, 34.16% w/v 3/4 EO/OH, Als oil

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 74446 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 89.34 Å2 / CC1/2: 0.982 / Net I/σ(I): 9.32
Reflection shellResolution: 3.5→3.56 Å / Num. unique obs: 3689 / CC1/2: 0.317

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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: 3.5→38.23 Å / SU ML: 0.504 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.3726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2689 2008 2.71 %
Rwork0.249 72194 -
obs0.2495 74202 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 149.11 Å2
Refinement stepCycle: LAST / Resolution: 3.5→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12152 0 10 0 12162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001912418
X-RAY DIFFRACTIONf_angle_d0.496616808
X-RAY DIFFRACTIONf_chiral_restr0.0381842
X-RAY DIFFRACTIONf_plane_restr0.00392218
X-RAY DIFFRACTIONf_dihedral_angle_d3.76721676
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.73115773242
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.22752251248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.39041350.36094990X-RAY DIFFRACTION97.23
3.59-3.690.34681480.35255194X-RAY DIFFRACTION99.93
3.69-3.80.29061450.33065160X-RAY DIFFRACTION99.81
3.8-3.920.35331500.31935133X-RAY DIFFRACTION99.42
3.92-4.060.3141370.29415180X-RAY DIFFRACTION99.44
4.06-4.220.30041360.28275112X-RAY DIFFRACTION99.6
4.22-4.410.28261440.27125159X-RAY DIFFRACTION99.53
4.41-4.650.32141460.26535160X-RAY DIFFRACTION99.55
4.65-4.940.23571420.21685147X-RAY DIFFRACTION99.81
4.94-5.320.2371470.21475183X-RAY DIFFRACTION99.93
5.32-5.850.23851460.23155200X-RAY DIFFRACTION99.93
5.85-6.690.28351470.2495174X-RAY DIFFRACTION99.92
6.69-8.420.26361400.23045218X-RAY DIFFRACTION99.94
8.42-38.230.19551450.17085184X-RAY DIFFRACTION99.05
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)
10.3602557501970.483713551251-0.09835248717211.432285764670.3494864086450.314267607828-0.162180842038-0.139013932242-0.5650844518570.625458210735-0.1706168580820.2064067910340.5985739370780.1649892122740.1060237193333.34819058870.9982886294330.5698599622651.969439447440.7293713159592.91425792683-5.25989521619-78.628237074245.807332314
21.96041339443-0.187521934367-0.428756534780.681451954936-0.1185292599392.189275098190.0199748725824-0.003700235899070.921170339667-0.5147559289760.0883170243233-0.758982486624-0.370422215377-0.120390360554-0.2453193571110.513992481443-0.0861187454642-0.06502229226710.5045522024460.07129782051451.05236818415-30.419359584-5.8344250220622.3204060812
30.996242989232-1.250382398650.5203587492332.85349163188-1.578070566350.9855023604980.3508300143540.1284908200771.05988235862-0.2541256749540.2454230572760.277258216354-1.03366127259-0.503688176609-0.05259568156771.603707558960.5585357616880.4574192531810.8456172180030.5886672371982.31631229445-57.458239081631.84329995999.51928523635
40.5817646101610.212083298751-0.8773108765211.333939789040.7517375968312.152160057270.05371976904171.46910653724-0.138262686732-1.59208850162-0.187273067601-0.1055874379980.4468301217920.02349544392650.1525720580251.528609675750.173394781930.1121850938152.20780652138-0.007845956722830.62354573113-32.8380987978-12.5773792848-11.5210550371
50.368187625939-0.1755820864280.3199946108680.136773013347-0.05519924318630.443655199978-0.02447175787240.1365454072030.174003113060.179684402235-0.0512002428597-0.2839206364120.1035414618670.1407030349080.1632587926953.236412504661.095833006741.034629625331.44730861771.057790892583.6485056648-72.867712636574.8226523355-2.15433837062
62.35208245045-2.71165223061-0.1837511530427.30441417994-1.679505355761.84274672258-0.229819237786-0.253047598510.5333929183640.8651572657220.7737197950970.351450152125-0.990448046158-0.569905266119-0.1103749285990.7376796679640.2083734328950.1564493149550.5432359718550.1294470714350.978090227094-42.56504769932.8866043233325.6806795985
70.4028321687340.244256634143-0.5170088078060.265429314695-0.1021124110920.838247703263-0.1289673721980.376100173847-0.1317141592880.0282400846359-0.223827201272-0.5312301483550.4966336511630.368566098580.1420408551510.6692373230220.193173662178-0.002326441404760.3950655888730.1233307724410.991250827984-35.806868561-32.492304952128.0216336622
85.613943069730.225378930643-0.6971032607893.97174974188-0.8900462514434.45326860956-0.106886583760.9108816383570.545461972945-0.4916331824420.2302951831520.0290055733440.0702359689149-0.505026726857-0.06834369217720.305151002070.00606205567667-0.1186912952390.49328647547-0.003625862233780.638317870906-70.3484357814-16.364130949714.0347876703
92.54916664850.836584782309-0.2373891186341.32029788397-0.03307118881822.03336824833-0.09197723999560.03194248419610.3398414626360.08249440618950.02932510493390.6556882671920.273040034852-0.161285037299-0.1956759080250.3637491326380.06685890514490.08174872946750.564435671502-0.005979606228180.977599223527-52.8990117871-23.174528808232.0075008687
100.7388636357061.338866648820.6449331837762.857641844411.726924637451.178277908560.09404448478340.0271334200421.13543367480.4606220602740.6187223461-0.39168969549-0.9327534079570.58325438465-0.1447551732931.49613967171-0.4814250469810.3738487011831.08872683989-0.7416532913062.51202865-19.809694410828.777423142658.4689136762
110.4643836904140.00648249995177-0.6116507680531.11208510694-0.8431895441641.996697344890.384602309152-1.88144277356-0.1349209162841.73582915366-0.285173233408-0.02994550620810.5464951252860.06045111482030.08337914389471.66929547411-0.2497054003820.2565323639282.737475652350.1786487741150.102570532219-44.4035542927-21.079588162772.5968345176
122.440894330952.811066759971.185873694593.579387277610.7655795721093.986752858980.335864438586-0.1709008860950.301218461105-0.1782492049340.2404721292950.9058634153350.13871562421-0.184286011463-0.1921516197762.8838999954-0.6144391652860.6980071023641.34603653442-0.7521684222443.93951518307-5.6959193565871.269816972773.9428065085
131.758824969271.88901164242-0.000271841903186.090550024911.752590548461.707961489460.1023702819730.02338422176580.509672818411-0.187945382970.394077502316-0.557725478647-0.6638394164670.5419771594540.04499654778470.634587926068-0.245948024020.2190530944620.628056913337-0.1497889406331.1222861818-34.84165946491.8846076071738.2314329491
140.6757151038360.0481582544863-0.7404761572390.420481989940.08484176274240.715324675863-0.149063576396-0.356096784665-0.20523124166-0.0912016316864-0.1652725864460.4992626427360.483999135385-0.4478473253740.1268309622350.759196338269-0.205465754423-0.1231629748540.501591503066-0.08357772487370.886947862038-41.6663961592-32.798537631130.3191346917
155.610457402550.587911409571-0.8462251961083.383028491011.262476449883.68573515644-0.302775441427-0.8181262241830.5048386879310.2650456715820.2095404976720.0235334075623-0.003257904540060.5184738444450.142314017310.314634044719-0.0272435775553-0.1588399767450.605818131336-0.01749041768660.59044069009-6.99636837264-19.462253765646.8913452374
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 118 )AA85 - 1181 - 34
22chain 'A' and (resid 119 through 231 )AA119 - 23135 - 147
33chain 'A' and (resid 232 through 284 )AA232 - 284148 - 196
44chain 'A' and (resid 285 through 470 )AA285 - 470197 - 382
55chain 'B' and (resid 85 through 122 )BB85 - 1221 - 38
66chain 'B' and (resid 123 through 231 )BB123 - 23139 - 147
77chain 'B' and (resid 232 through 305 )BB232 - 305148 - 221
88chain 'B' and (resid 306 through 470 )BB306 - 470222 - 386
99chain 'C' and (resid 85 through 231 )CC85 - 2311 - 147
1010chain 'C' and (resid 232 through 283 )CC232 - 283148 - 195
1111chain 'C' and (resid 284 through 470 )CC284 - 470196 - 382
1212chain 'D' and (resid 85 through 122 )DD85 - 1221 - 38
1313chain 'D' and (resid 123 through 231 )DD123 - 23139 - 147
1414chain 'D' and (resid 232 through 305 )DD232 - 305148 - 221
1515chain 'D' and (resid 306 through 470 )DD306 - 470222 - 386

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