[English] 日本語
Yorodumi
- PDB-7xz1: TRIM E3 ubiquitin ligase -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / sarcolemma / protein homooligomerization / 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
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, 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more