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- PDB-8a58: X-ray structure of TRIM21 RING E3 ligase in complex with E2 enzym... -

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Basic information

Entry
Database: PDB / ID: 8a58
TitleX-ray structure of TRIM21 RING E3 ligase in complex with E2 enzyme Ube2W
Components
  • E3 ubiquitin-protein ligase TRIM21
  • Ubiquitin-conjugating enzyme E2 W
KeywordsLIGASE / E3 ubiquitin ligase
Function / homology
Function and homology information


N-terminal E2 ubiquitin-conjugating enzyme / negative regulation of protein deubiquitination / regulation of viral entry into host cell / protein K27-linked ubiquitination / suppression of viral release by host / regulation of type I interferon production / cellular response to chemical stress / negative regulation of viral transcription / protein K6-linked ubiquitination / STING mediated induction of host immune responses ...N-terminal E2 ubiquitin-conjugating enzyme / negative regulation of protein deubiquitination / regulation of viral entry into host cell / protein K27-linked ubiquitination / suppression of viral release by host / regulation of type I interferon production / cellular response to chemical stress / negative regulation of viral transcription / protein K6-linked ubiquitination / STING mediated induction of host immune responses / protein K11-linked ubiquitination / cellular response to misfolded protein / stress granule disassembly / E2 ubiquitin-conjugating enzyme / negative regulation of NF-kappaB transcription factor activity / pyroptotic inflammatory response / protein quality control for misfolded or incompletely synthesized proteins / response to type II interferon / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / antiviral innate immune response / autophagosome / proteasomal protein catabolic process / protein autoubiquitination / protein K48-linked ubiquitination / positive regulation of autophagy / positive regulation of cell cycle / negative regulation of TORC1 signaling / Regulation of innate immune responses to cytosolic DNA / negative regulation of innate immune response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / P-body / protein destabilization / RING-type E3 ubiquitin transferase / positive regulation of DNA-binding transcription factor activity / cytoplasmic stress granule / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of protein localization / Interferon gamma signaling / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of protein binding / cytoplasmic vesicle / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / positive regulation of viral entry into host cell / protein ubiquitination / ribonucleoprotein complex / cell cycle / DNA repair / innate immune response / ubiquitin protein ligase binding / protein kinase binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / Modified RING finger domain / U-box domain / B-box zinc finger / B-Box-type zinc finger ...TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / Modified RING finger domain / U-box domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / 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
E3 ubiquitin-protein ligase TRIM21 / Ubiquitin-conjugating enzyme E2 W
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJames, L.C. / Kiss, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
Citation
Journal: Nat Commun / Year: 2023
Title: Trim-Away ubiquitinates and degrades lysine-less and N-terminally acetylated substrates.
Authors: Kiss, L. / Rhinesmith, T. / Luptak, J. / Dickson, C.F. / Weidenhausen, J. / Smyly, S. / Yang, J.C. / Maslen, S.L. / Sinning, I. / Neuhaus, D. / Clift, D. / James, L.C.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: James, L.C. / Kiss, L.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 W
C: E3 ubiquitin-protein ligase TRIM21
D: E3 ubiquitin-protein ligase TRIM21
B: Ubiquitin-conjugating enzyme E2 W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5148
Polymers54,2534
Non-polymers2624
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-23 kcal/mol
Surface area24580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.820, 75.482, 63.835
Angle α, β, γ (deg.)90.000, 119.310, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 26 or (resid 32...
21(chain B and (resid 2 through 26 or resid 32...
12(chain C and ((resid 5 through 7 and (name N...
22(chain D and (resid 5 through 44 or resid 46...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAASNASN(chain A and (resid 2 through 26 or (resid 32...AA2 - 264 - 28
121ASNASNASNASN(chain A and (resid 2 through 26 or (resid 32...AA3234
131ALAALATRPTRP(chain A and (resid 2 through 26 or (resid 32...AA2 - 1454 - 147
141ALAALATRPTRP(chain A and (resid 2 through 26 or (resid 32...AA2 - 1454 - 147
151ALAALATRPTRP(chain A and (resid 2 through 26 or (resid 32...AA2 - 1454 - 147
161ALAALATRPTRP(chain A and (resid 2 through 26 or (resid 32...AA2 - 1454 - 147
211ALAALAASNASN(chain B and (resid 2 through 26 or resid 32...BD2 - 264 - 28
221ASNASNSERSER(chain B and (resid 2 through 26 or resid 32...BD32 - 6234 - 64
231TYRTYRPROPRO(chain B and (resid 2 through 26 or resid 32...BD64 - 6966 - 71
241VALVALILEILE(chain B and (resid 2 through 26 or resid 32...BD71 - 9073 - 92
251LYSLYSLYSLYS(chain B and (resid 2 through 26 or resid 32...BD9193
261SERSERHISHIS(chain B and (resid 2 through 26 or resid 32...BD-1 - 1471 - 149
271SERSERHISHIS(chain B and (resid 2 through 26 or resid 32...BD-1 - 1471 - 149
281SERSERHISHIS(chain B and (resid 2 through 26 or resid 32...BD-1 - 1471 - 149
291SERSERHISHIS(chain B and (resid 2 through 26 or resid 32...BD-1 - 1471 - 149
112ALAALALEULEU(chain C and ((resid 5 through 7 and (name N...CB5 - 75 - 7
122METMETGLUGLU(chain C and ((resid 5 through 7 and (name N...CB1 - 821 - 82
132METMETGLUGLU(chain C and ((resid 5 through 7 and (name N...CB1 - 821 - 82
142METMETGLUGLU(chain C and ((resid 5 through 7 and (name N...CB1 - 821 - 82
152METMETGLUGLU(chain C and ((resid 5 through 7 and (name N...CB1 - 821 - 82
212ALAALAGLYGLY(chain D and (resid 5 through 44 or resid 46...DC5 - 445 - 44
222GLYGLYASNASN(chain D and (resid 5 through 44 or resid 46...DC46 - 6646 - 66
232GLNGLNLYSLYS(chain D and (resid 5 through 44 or resid 46...DC68 - 7768 - 77
242GLUGLUGLUGLU(chain D and (resid 5 through 44 or resid 46...DC7878
252ALAALAZNZN(chain D and (resid 5 through 44 or resid 46...DC - H5 - 1025
262ALAALAZNZN(chain D and (resid 5 through 44 or resid 46...DC - H5 - 1025
272ALAALAZNZN(chain D and (resid 5 through 44 or resid 46...DC - H5 - 1025
282ALAALAZNZN(chain D and (resid 5 through 44 or resid 46...DC - H5 - 1025

NCS ensembles :
ID
1
2

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 W / E2 ubiquitin-conjugating enzyme W / N-terminal E2 ubiquitin-conjugating enzyme / N-terminus- ...E2 ubiquitin-conjugating enzyme W / N-terminal E2 ubiquitin-conjugating enzyme / N-terminus-conjugating E2 / Ubiquitin carrier protein W / Ubiquitin-conjugating enzyme 16 / UBC-16 / Ubiquitin-protein ligase W


Mass: 17616.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2W, UBC16 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96B02, E2 ubiquitin-conjugating enzyme, N-terminal E2 ubiquitin-conjugating enzyme
#2: Protein E3 ubiquitin-protein ligase TRIM21 / 52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / RING- ...52 kDa Ro protein / 52 kDa ribonucleoprotein autoantigen Ro/SS-A / RING finger protein 81 / RING-type E3 ubiquitin transferase TRIM21 / Ro(SS-A) / Sjoegren syndrome type A antigen / SS-A / Tripartite motif-containing protein 21


Mass: 9510.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM21, RNF81, RO52, SSA1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P19474, RING-type E3 ubiquitin transferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bicine pH 9.0, 5% PEG 6000, 0.1M TCEP hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.984004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984004 Å / Relative weight: 1
ReflectionResolution: 2.25→29.46 Å / Num. obs: 23652 / % possible obs: 95.32 % / Redundancy: 3.3 % / Biso Wilson estimate: 60.75 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.49
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 2357 / CC1/2: 0.859

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OLM

5olm


Resolution: 2.25→29.46 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 1191 5.04 %
Rwork0.2153 22458 -
obs0.2174 23649 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.2 Å2 / Biso mean: 82.8586 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.25→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3445 0 4 35 3484
Biso mean--56.94 78.61 -
Num. residues----451
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A792X-RAY DIFFRACTION12.988TORSIONAL
12B792X-RAY DIFFRACTION12.988TORSIONAL
21C0X-RAY DIFFRACTION12.988TORSIONAL
22D0X-RAY DIFFRACTION12.988TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.340.42061510.35042485263696
2.34-2.450.40791480.33052456260495
2.45-2.580.431340.32662453258795
2.58-2.740.37461480.30072480262895
2.74-2.950.28171120.23982541265397
2.95-3.240.28411210.22852536265797
3.24-3.710.29011090.21362504261394
3.71-4.670.23591170.18692495261294
4.67-29.460.20831510.18692508265994

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