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- PDB-7xz0: TRIM E3 ubiquitin ligase -

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Basic information

Entry
Database: PDB / ID: 7xz0
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 / plasma membrane repair / vesicle budding from membrane / ubiquitin conjugating enzyme binding / mitogen-activated protein kinase kinase kinase 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 / plasma membrane repair / vesicle budding from membrane / ubiquitin conjugating enzyme binding / mitogen-activated protein kinase kinase kinase binding / muscle organ development / phosphatidylserine binding / exocytosis / negative regulation of insulin receptor signaling pathway / cytoplasmic vesicle membrane / protein homooligomerization / sarcolemma / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / zinc ion binding / identical protein binding
Similarity search - Function
SPRY domain / 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 ...SPRY domain / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / 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 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tripartite motif-containing protein 72
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 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)88,6636
Polymers88,4012
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Dimer, cross-linking, Dimer, Higher-order assembly in the liposome, electron microscopy, Higher-order assembly in the liposome, gel filtration, Dimer, Higher-order assembly in the liposome
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-93 kcal/mol
Surface area42290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)239.728, 72.967, 83.764
Angle α, β, γ (deg.)90.000, 97.600, 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_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: ARG / End label comp-ID: ARG / Auth seq-ID: 85 - 386 / Label seq-ID: 9 - 310

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.126394169972, 0.353672994327, -0.926790120189), (0.360635564223, -0.886736862431, -0.289205336435), (-0.924103080622, -0.297679609461, -0.23962542957)Vector: -7. ...NCS oper: (Code: given
Matrix: (0.126394169972, 0.353672994327, -0.926790120189), (0.360635564223, -0.886736862431, -0.289205336435), (-0.924103080622, -0.297679609461, -0.23962542957)
Vector: -7.79247513259, 50.3149817894, 9.19674248773)

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Components

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


Mass: 44200.523 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

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM TRIS-HCl pH 8.5, 8% (v/v) PEG 8000

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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: 3.28→50 Å / Num. obs: 22376 / % possible obs: 98.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 100.76 Å2 / CC1/2: 0.995 / Net I/σ(I): 21.5
Reflection shellResolution: 3.28→3.34 Å / Num. unique obs: 1110 / CC1/2: 0.558

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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: 3.28→37.74 Å / SU ML: 0.5585 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.2094
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3078 1941 8.96 %
Rwork0.2541 19711 -
obs0.2588 21652 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 139.02 Å2
Refinement stepCycle: LAST / Resolution: 3.28→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 4 0 6112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00276242
X-RAY DIFFRACTIONf_angle_d0.65048450
X-RAY DIFFRACTIONf_chiral_restr0.0446926
X-RAY DIFFRACTIONf_plane_restr0.0041116
X-RAY DIFFRACTIONf_dihedral_angle_d4.8515844
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.83355620019 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.360.47311390.45111413X-RAY DIFFRACTION97.3
3.36-3.450.36961390.35431422X-RAY DIFFRACTION98.55
3.45-3.550.38431360.31371379X-RAY DIFFRACTION98.31
3.55-3.670.40941410.33111427X-RAY DIFFRACTION98.55
3.67-3.80.40461400.34441436X-RAY DIFFRACTION98.69
3.8-3.950.41211360.32771368X-RAY DIFFRACTION96.47
3.95-4.130.31731350.28621366X-RAY DIFFRACTION94.76
4.13-4.350.36081370.2871353X-RAY DIFFRACTION94.48
4.35-4.620.28981350.25221395X-RAY DIFFRACTION95.74
4.62-4.980.24371370.22931389X-RAY DIFFRACTION96.46
4.98-5.480.30771390.21491429X-RAY DIFFRACTION98.62
5.48-6.270.3281420.26521449X-RAY DIFFRACTION99.19
6.27-7.880.32821440.25251460X-RAY DIFFRACTION99.38
7.89-37.740.20431410.1711425X-RAY DIFFRACTION94.34
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)
11.54770355412-0.8410274702690.005499540714411.458617471180.5320479444940.9159820771170.533996682836-0.0048624517071-0.850050699382-0.3682160430440.0174362067141.088794170210.402840710598-0.258931956395-0.6509911404510.688402317346-0.146372353727-0.2087201879990.6233467868720.2092190641551.24518051382-75.763242514510.584287690449.4397106817
21.72028646814-1.978697753522.274360091123.37311453562-4.742772969156.81495245491-0.4169418776550.5989056112950.42919603470.19595392281-1.44581608328-1.599357419590.6901397458471.787036015661.279986401330.9350159158840.0699068369556-0.2802885145470.6650170634870.2162140520971.21343130682-44.9406968254-0.53528591484458.8691457078
34.90458346964-1.28242690971-1.632397913125.455918954112.688622665918.49160663594-0.007880006964921.096938123950.263685417195-1.72765869951-0.0189100526881-0.897364868287-0.07833554571270.48605393807-0.006687757873531.06760022283-0.03528420542710.2902294688950.849224598768-0.009115930225680.606920187302-47.5222184838-4.0833850365322.4760814259
41.24045623016-0.548226081649-0.06654406274810.6812364483980.8331703484941.769056652450.9891220052631.00491237637-0.981071509241-0.941083883076-0.3229501632950.3693364782070.7271593281910.05043533509-0.7893207877942.295507169810.811487270901-0.693224466572.41213292430.6792962896292.80972017695-19.0865928414-43.948973270795.5665468228
5-0.0045661168266-0.594182108406-0.09639501709872.90535283198-0.5585672491141.04192584215-0.76419945219-0.7518122480890.183316417540.6816889510530.5040071481430.378314393329-0.505987769145-0.5456476262520.2684815126860.8091995191490.228172893948-0.03906327737070.9174208912390.1440806133330.922046539429-70.607306100510.370704017755.7150466621
60.479136411687-0.18541488394-0.1198810164682.344955822050.08106534194781.53365899085-0.3707127614750.0709340133581.802024259540.0527223315482-0.412896409827-0.960561078878-0.4494328127920.2382280993010.53088557851.12429632861-0.137360432151-0.5208653588690.5602914167540.1926318959032.04482578272-52.300398401830.495721947945.7585160459
77.057701344943.967547216850.1278219272067.122583937352.839841038744.736008548310.08500918095110.2952760347640.4763373671160.123153634324-0.0542685662602-2.66372030428-0.4001883336260.903812514343-0.1002438258771.13168592484-0.193406727086-0.4522151742310.9312509033160.2577433343192.21384253124-34.737081728626.948111365748.3634085979
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 253 )AA85 - 2531 - 169
22chain 'A' and (resid 254 through 284 )AA254 - 284170 - 200
33chain 'A' and (resid 285 through 470 )AA285 - 470201 - 386
44chain 'B' and (resid 85 through 118 )BB85 - 1181 - 34
55chain 'B' and (resid 119 through 252 )BB119 - 25235 - 168
66chain 'B' and (resid 253 through 323 )BB253 - 323169 - 239
77chain 'B' and (resid 324 through 470 )BB324 - 470240 - 386

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