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- PDB-7xt2: Crystal structure of TRIM72 -

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Basic information

Entry
Database: PDB / ID: 7xt2
TitleCrystal structure of TRIM72
ComponentsTripartite motif-containing protein 72
KeywordsLIGASE / TRIM72 / MG53 / B-Box / CC / SPRY
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 / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / muscle organ development / phosphatidylserine binding / exocytosis / Smooth Muscle Contraction ...muscle system process / negative regulation of insulin-like growth factor receptor signaling pathway / negative regulation of myotube differentiation / plasma membrane repair / mitogen-activated protein kinase kinase kinase binding / ubiquitin conjugating enzyme binding / muscle organ development / phosphatidylserine binding / exocytosis / Smooth Muscle Contraction / 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 of C3HC4-type, RING / 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 ...zinc finger of C3HC4-type, RING / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhou, C. / Ma, Y.M. / Ding, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for TRIM72 oligomerization during membrane damage repair.
Authors: Ma, Y. / Ding, L. / Li, Z. / Zhou, C.
History
DepositionMay 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,8636
Polymers105,6012
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, TRIM family proteins are dimers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10880 Å2
ΔGint-90 kcal/mol
Surface area41210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.571, 125.231, 174.537
Angle α, β, γ (deg.)90.000, 91.450, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 84 through 602)
21(chain B and (resid 84 through 396 or resid 398 through 602))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYZNZN(chain A and resid 84 through 602)AB - F84 - 60284
21GLYGLYGLUGLU(chain B and (resid 84 through 396 or resid 398 through 602))BA84 - 39684 - 396
22LYSLYSZNZN(chain B and (resid 84 through 396 or resid 398 through 602))BA - D398 - 602398

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Components

#1: Protein Tripartite motif-containing protein 72 / Mitsugumin-53 / Mg53 / TRIM72


Mass: 52800.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM72, MG53 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZMU5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 3.75 Å3/Da / Density % sol: 72.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3→43.14 Å / Num. obs: 60046 / % possible obs: 98.57 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0972 / Rpim(I) all: 0.03994 / Net I/σ(I): 13.14
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 3064 / CC1/2: 0.51 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KB5

3kb5


Resolution: 3→43.14 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 2758 4.59 %
Rwork0.2188 57288 -
obs0.2206 60046 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.18 Å2 / Biso mean: 140.196 Å2 / Biso min: 69.1 Å2
Refinement stepCycle: final / Resolution: 3→43.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6138 0 4 0 6142
Biso mean--151.65 --
Num. residues----776
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2376X-RAY DIFFRACTION8.639TORSIONAL
12B2376X-RAY DIFFRACTION8.639TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.050.48731100.43442843295397
3.05-3.110.46341600.4332833299398
3.11-3.170.42921480.40352945309399
3.17-3.230.4019950.38772885298099
3.23-3.30.41531330.36952991312498
3.3-3.380.36151370.34992780291798
3.38-3.460.39961250.3472816294193
3.46-3.560.3971080.30612842295098
3.56-3.660.39111070.27592930303799
3.66-3.780.2873880.2622923301197
3.78-3.910.30721610.26032851301298
3.91-4.070.2571430.22232921306499
4.07-4.260.22031620.2122920308299
4.26-4.480.25711700.19382795296597
4.48-4.760.19951480.18832774292297
4.76-5.130.23551360.17382932306899
5.13-5.640.2485840.21282954303899
5.64-6.460.25151800.21492819299998
6.46-8.120.22772140.19692772298697
8.13-43.140.17771490.13522762291195
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)
10.9477-0.03410.69170.16140.37711.2739-0.0598-0.2207-0.18470.3058-0.0942-0.12261.7874-1.66440.151.4153-0.2793-0.02840.52610.0910.939319.322-23.137129.819
21.1035-1.2742-2.63851.39322.76666.10660.51170.16450.1653-0.5817-0.2180.3701-0.9411-0.01510.15330.82560.0568-0.09911.13170.0650.887614.247-5.662100.673
39.4871.62671.41545.52510.44136.3494-0.0151-0.48831.0670.0389-0.05180.4929-0.3815-0.41920.07730.59530.08110.07640.7925-0.0010.8634-17.647-0.625117.784
40.5910.2992-0.84860.75950.44563.93710.1144-0.094-0.01210.040.1734-0.10550.6110.3134-0.16980.63080.1098-0.12830.96830.0940.872325.171-19.08394.277
50.0785-0.32860.79671.0159-1.38474.73190.0475-0.5589-0.60891.01870.3931-0.00231.2366-2.28-0.72482.2525-0.1488-0.00991.90720.36841.231512.833-22.905169.868
63.64142.9276-0.26518.5253-0.1975.62420.1125-0.14480.7878-0.06890.0384-0.3755-1.693-0.111-0.11891.04510.10920.08220.7189-0.06150.939621.11819.275116.599
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 84:254 )B84 - 254
2X-RAY DIFFRACTION2( CHAIN B AND RESID 255:284 )B255 - 284
3X-RAY DIFFRACTION3( CHAIN B AND RESID 285:471 )B285 - 471
4X-RAY DIFFRACTION4( CHAIN A AND RESID 83:231 )A83 - 231
5X-RAY DIFFRACTION5( CHAIN A AND RESID 232:270 )A232 - 270
6X-RAY DIFFRACTION6( CHAIN A AND RESID 271:471 )A271 - 471

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