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- PDB-7xz1: TRIM E3 ubiquitin ligase -

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Basic information

Entry
Database: PDB / ID: 7xz1
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: 5.2 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
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

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)103,8946
Polymers103,6332
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Dimer, cross-linking, Dimer, Higher-order assembly on the liposome, electron microscopy, Higher-order assembly on the liposome, gel filtration, Dimer, Higher-order assembly on the ...Evidence: SAXS, Dimer, cross-linking, Dimer, Higher-order assembly on the liposome, electron microscopy, Higher-order assembly on the liposome, gel filtration, Dimer, Higher-order assembly on the liposome, light scattering, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-89 kcal/mol
Surface area45520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.921, 235.921, 158.814
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 85 - 470 / Label seq-ID: 81 - 466

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.924000307082, -0.203576474116, -0.323697469404), (-0.139832270652, -0.607996576656, 0.781528693561), (-0.355907809126, 0.767396104995, 0.533322462908)Vector: 83. ...NCS oper: (Code: given
Matrix: (-0.924000307082, -0.203576474116, -0.323697469404), (-0.139832270652, -0.607996576656, 0.781528693561), (-0.355907809126, 0.767396104995, 0.533322462908)
Vector: 83.3997032738, 21.571292693, 5.55601438451)

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Components

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


Mass: 51816.363 Da / Num. of mol.: 2 / Mutation: C55S, C144S, 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.: 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

CrystalDensity Matthews: 5.33 Å3/Da / Density % sol: 76.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM Hepes-NaOH pH 7.5, 250 mM MgCl2, 37% (w/v) 5/4 PO/OH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00933 Å / Relative weight: 1
ReflectionResolution: 5.2→50 Å / Num. obs: 9007 / % possible obs: 99.9 % / Redundancy: 28.8 % / Biso Wilson estimate: 311.87 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.135 / Net I/σ(I): 49.84
Reflection shellResolution: 5.2→5.29 Å / Num. unique obs: 452 / CC1/2: 0.523

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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: 5.2→38.86 Å / SU ML: 0.995 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 47.1228
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3152 880 10 %
Rwork0.2659 7923 -
obs0.2709 8803 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 443.99 Å2
Refinement stepCycle: LAST / Resolution: 5.2→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 4 0 6048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226176
X-RAY DIFFRACTIONf_angle_d0.69098358
X-RAY DIFFRACTIONf_chiral_restr0.0411916
X-RAY DIFFRACTIONf_plane_restr0.00491102
X-RAY DIFFRACTIONf_dihedral_angle_d4.1919832
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.53161190837 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.2-5.530.4871410.42841287X-RAY DIFFRACTION98.48
5.53-5.950.46371440.39921296X-RAY DIFFRACTION98.7
5.95-6.550.42231440.33111292X-RAY DIFFRACTION99.1
6.55-7.490.35861460.28581316X-RAY DIFFRACTION99.46
7.49-9.410.32281490.27641335X-RAY DIFFRACTION99.6
9.41-38.860.26441560.2271397X-RAY DIFFRACTION99.23
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)
12.391778559371.05409919748-3.714872562544.44117941179-3.092936495847.03339836358-2.46935163421-2.12456783679-5.90027780643-0.3332105785690.12283304254-2.58965212333-0.2317412414710.9575821428562.541272619434.971170867890.874925132741-0.3528347167093.005215054150.2211106882414.87235649824-4.9966353516748.7985781905-62.8848573162
24.97523185329-5.315739533826.14543189685.32810984493-4.873860327717.741513981730.917259879663-0.967994500379-0.688669339012-0.590192239361-0.6570231801282.624589033340.4882113637440.728752463045-0.01016077864193.80916529344-1.30076938729-0.03405094275135.350667410751.138273946025.4733710394552.3790760831-0.157828476547-24.5418789825
3-0.827020654021-1.05312913231.073850962950.193100247358-0.138588812841-0.365372053305-0.595951452831-2.211691971131.145526237372.168216835941.00343349994-1.69345597462-0.4661718655520.366426062782-0.6389817977713.583256696040.234972933590.7182852199514.94011563878-0.4618109189244.9001437028968.3138868465-14.7737135032-3.04937953775
45.36065516094-0.631024800583-0.9726593852199.55144839443-6.34209060214.481899860530.320475601273-2.00435655029-0.221809768133-0.07289997845291.43215359852-0.193093806466-0.05835548064170.248744581425-1.755911447424.28234339546-0.0179418064657-0.2437232344174.25228514081-0.6889027483514.5206975474856.109954006228.3649995327-0.411300265387
58.9460506432-5.802041024034.238684272342.05812043352-2.645594621733.58349061385-1.14582702182-0.6020989096020.06672590318040.5229808749920.614621738915-0.696813471653-0.926381124545-0.2890306233880.8458100397943.91380953624-1.10451299216-0.7743854078583.232421034160.5982417556643.7425589964854.7999636005-13.6991272149-20.3805362333
62.65779619135-0.126418641679-0.7208582135346.05845015276-1.385540051550.4605072414660.497553792184-1.28896974240.3807312706592.02007842686-0.6013740076761.04810279437-1.642244570380.1782638870730.004056161563693.6154978608-0.08519886725320.09880224709054.40896985361-0.2776238831993.0688059095226.4533925923-0.7193548333261.421811054
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 132 )AA85 - 1321 - 48
22chain 'A' and (resid 133 through 229 )AA133 - 22949 - 145
33chain 'A' and (resid 230 through 302 )AA230 - 302146 - 214
44chain 'A' and (resid 303 through 470 )AA303 - 470215 - 382
55chain 'B' and (resid 85 through 251 )BB85 - 2511 - 167
66chain 'B' and (resid 252 through 470 )BB252 - 470168 - 382

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