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- PDB-7zj3: Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate -

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Basic information

Entry
Database: PDB / ID: 7zj3
TitleStructure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate
Components
  • Polyubiquitin-C
  • Tripartite motif-containing protein 2
  • Ubiquitin-conjugating enzyme E2 D1
KeywordsLIGASE / Ubiquitin ligase / TRIM protein / RING ligase
Function / homology
Function and homology information


positive regulation of protein polyubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / Signaling by BMP / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity ...positive regulation of protein polyubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / (E3-independent) E2 ubiquitin-conjugating enzyme / Phosphorylation of the APC/C / Signaling by BMP / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / regulation of neuron apoptotic process / ubiquitin ligase complex / translation repressor activity / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of TORC1 signaling / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / positive regulation of protein ubiquitination / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD
Similarity search - Function
: / NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains ...: / NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D1 / Tripartite motif-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsEsposito, D. / Garza-Garcia, A. / Dudley-Fraser, J. / Rittinger, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001142 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Divergent self-association properties of paralogous proteins TRIM2 and TRIM3 regulate their E3 ligase activity.
Authors: Esposito, D. / Dudley-Fraser, J. / Garza-Garcia, A. / Rittinger, K.
History
DepositionApr 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Tripartite motif-containing protein 2
E: Ubiquitin-conjugating enzyme E2 D1
F: Polyubiquitin-C
G: Tripartite motif-containing protein 2
H: Ubiquitin-conjugating enzyme E2 D1
I: Polyubiquitin-C
J: Tripartite motif-containing protein 2
K: Ubiquitin-conjugating enzyme E2 D1
L: Polyubiquitin-C
A: Tripartite motif-containing protein 2
C: Polyubiquitin-C
B: Ubiquitin-conjugating enzyme E2 D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,64320
Polymers146,12012
Non-polymers5238
Water2,486138
1
D: Tripartite motif-containing protein 2
E: Ubiquitin-conjugating enzyme E2 D1
F: Polyubiquitin-C
J: Tripartite motif-containing protein 2
K: Ubiquitin-conjugating enzyme E2 D1
L: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,32210
Polymers73,0606
Non-polymers2624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Tripartite motif-containing protein 2
H: Ubiquitin-conjugating enzyme E2 D1
I: Polyubiquitin-C
A: Tripartite motif-containing protein 2
C: Polyubiquitin-C
B: Ubiquitin-conjugating enzyme E2 D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,32210
Polymers73,0606
Non-polymers2624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.319, 123.662, 112.471
Angle α, β, γ (deg.)90.000, 102.803, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 9 through 93)
d_2ens_1chain "D"
d_3ens_1chain "G"
d_4ens_1chain "J"
d_1ens_2(chain "B" and resid 1 through 145)
d_2ens_2(chain "E" and resid 1 through 145)
d_3ens_2(chain "H" and resid 1 through 145)
d_4ens_2chain "K"
d_1ens_3(chain "C" and resid 3 through 76)
d_2ens_3(chain "F" and resid 3 through 76)
d_3ens_3chain "I"
d_4ens_3(chain "L" and resid 3 through 76)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROTHRR1 - 85
d_21ens_1PROTHRA1 - 85
d_31ens_1PROTHRD1 - 85
d_41ens_1PROTHRG1 - 85
d_11ens_2SERTYRT2 - 146
d_21ens_2SERTYRB2 - 146
d_31ens_2SERTYRE5 - 149
d_41ens_2SERTYRH1 - 145
d_11ens_3ILEGLYS3 - 76
d_21ens_3ILEGLYC4 - 77
d_31ens_3ILEGLYF1 - 74
d_41ens_3ILEGLYI4 - 77

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.313048437548, -0.0289663322592, -0.949295331993), (0.022513141824, -0.999480250774, 0.0230735077062), (-0.94947029137, -0.0141484949058, 0.313537854012)21.4405296804, 27.8293043647, -27.8025270919
2given(0.146095375386, -0.0270616351195, -0.988900302961), (-0.0162579447789, -0.999556455712, 0.0249513742351), (-0.989136906865, 0.0124322061321, -0.146470542186)25.0188763286, 41.164527551, 28.0391100599
3given(0.90165197757, 0.0327473548852, 0.431220734767), (-0.00623279177591, 0.998009339723, -0.0627575504012), (-0.432417464554, 0.0538977603774, 0.900061202238)-14.1764573117, -11.7608517463, -43.7836868931
4given(-0.342489282409, -0.00248815043308, -0.939518440767), (-0.00962195210237, -0.999934760505, 0.0061557105506), (-0.939472463392, 0.0111482663256, 0.342442997717)20.7124318483, 28.7280161858, -29.4114528559
5given(0.173299468915, -0.0201054063076, -0.984663935925), (0.00795674169318, -0.99973039621, 0.0218134168826), (-0.984837034405, -0.0116149701537, -0.173092773197)24.3298852193, 40.6742085324, 29.3648212871
6given(0.924517601263, 0.00469405268306, 0.381110444391), (0.00352588615675, 0.999776036922, -0.0208672979646), (-0.381123041918, 0.0206359362992, 0.92429399276)-12.8258168098, -12.602216833, -43.6937789235
7given(-0.376991755182, -0.0203036759312, -0.925994048182), (0.0252160338349, -0.999614117801, 0.0116519153348), (-0.925873300275, -0.0189572212366, 0.377358258954)21.7998130782, 28.1399287197, -28.6020308477
8given(0.164814574362, -0.0257106671869, -0.985989410527), (0.019409734952, -0.999382067468, 0.0293043582672), (-0.986133570196, -0.0239675784586, -0.164213692839)24.5178881574, 40.5384058625, 29.5527136467
9given(0.929471664662, 0.02199974702, 0.368236928785), (-0.0166642047335, 0.999705109025, -0.0176635010527), (-0.368516931593, 0.0102813481555, 0.929564180146)-13.5482260841, -12.2086305895, -43.4252842935

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Components

#1: Protein
Tripartite motif-containing protein 2 / E3 ubiquitin-protein ligase TRIM2 / RING finger protein 86 / RING-type E3 ubiquitin transferase TRIM2


Mass: 10769.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM2, KIAA0517, RNF86 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9C040, RING-type E3 ubiquitin transferase
#2: Protein
Ubiquitin-conjugating enzyme E2 D1 / (E3-independent) E2 ubiquitin-conjugating enzyme D1 / E2 ubiquitin-conjugating enzyme D1 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D1 / E2 ubiquitin-conjugating enzyme D1 / Stimulator of Fe transport / SFT / UBC4/5 homolog / UbcH5 / Ubiquitin carrier protein D1 / Ubiquitin-conjugating enzyme E2(17)KB 1 / Ubiquitin-conjugating enzyme E2-17 kDa 1 / Ubiquitin-protein ligase D1


Mass: 16867.225 Da / Num. of mol.: 4 / Mutation: S22R C85K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A / Production host: Escherichia coli (E. coli)
References: UniProt: P51668, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#3: Protein
Polyubiquitin-C


Mass: 8893.206 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5 10% (w/v) PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.2821 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2821 Å / Relative weight: 1
ReflectionResolution: 2.53→109.675 Å / Num. obs: 51031 / % possible obs: 99.79 % / Redundancy: 6.5 % / Biso Wilson estimate: 42.64 Å2 / CC1/2: 0.99 / CC star: 0.998 / Net I/σ(I): 4.11
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 0.38 / Num. unique obs: 5126 / CC1/2: 0.537 / CC star: 0.836 / % possible all: 99.71

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PHENIX1.20.1-4487refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FER

5fer


Resolution: 2.53→54.97 Å / SU ML: 0.3725 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.5502
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2576 2561 5.03 %
Rwork0.2105 48389 -
obs0.2129 50950 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.93 Å2
Refinement stepCycle: LAST / Resolution: 2.53→54.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9804 0 8 138 9950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005410034
X-RAY DIFFRACTIONf_angle_d0.832713620
X-RAY DIFFRACTIONf_chiral_restr0.05141541
X-RAY DIFFRACTIONf_plane_restr0.00591755
X-RAY DIFFRACTIONf_dihedral_angle_d18.45823828
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2JX-RAY DIFFRACTIONTorsion NCS0.71836146644
ens_1d_3JX-RAY DIFFRACTIONTorsion NCS0.965266225707
ens_1d_4JX-RAY DIFFRACTIONTorsion NCS0.891613321716
ens_2d_2KX-RAY DIFFRACTIONTorsion NCS0.803394087719
ens_2d_3KX-RAY DIFFRACTIONTorsion NCS0.682375270282
ens_2d_4KX-RAY DIFFRACTIONTorsion NCS0.83100511001
ens_3d_2LX-RAY DIFFRACTIONTorsion NCS0.687181831694
ens_3d_3LX-RAY DIFFRACTIONTorsion NCS0.852915005288
ens_3d_4LX-RAY DIFFRACTIONTorsion NCS0.852583859473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.580.37321570.33542673X-RAY DIFFRACTION99.58
2.58-2.630.37191490.31782656X-RAY DIFFRACTION99.68
2.63-2.690.35821620.2982657X-RAY DIFFRACTION99.75
2.69-2.750.35961320.27382673X-RAY DIFFRACTION99.82
2.75-2.820.35311420.26392669X-RAY DIFFRACTION99.65
2.82-2.90.31491420.262708X-RAY DIFFRACTION99.96
2.9-2.980.28241320.25652679X-RAY DIFFRACTION99.79
2.98-3.080.2881350.24582676X-RAY DIFFRACTION99.89
3.08-3.190.29061560.24282692X-RAY DIFFRACTION99.93
3.19-3.320.29521200.22382692X-RAY DIFFRACTION99.82
3.32-3.470.25211250.23022696X-RAY DIFFRACTION99.89
3.47-3.650.27211460.2172679X-RAY DIFFRACTION99.93
3.65-3.880.28251550.20242692X-RAY DIFFRACTION99.96
3.88-4.180.21031640.17812674X-RAY DIFFRACTION99.86
4.18-4.60.18841430.16542682X-RAY DIFFRACTION99.89
4.6-5.260.2081270.1642739X-RAY DIFFRACTION99.9
5.26-6.630.24791300.19832716X-RAY DIFFRACTION100
6.63-54.970.20391440.16892736X-RAY DIFFRACTION99.14

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