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- PDB-6fga: Crystal structure of TRIM21 E3 ligase, RING domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6fga
TitleCrystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1
Components
  • E3 ubiquitin-protein ligase TRIM21
  • Ubiquitin-conjugating enzyme E2 E1
KeywordsLIGASE / RING-type E3 ligase / UBC core domain and Ubiquitination
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / suppression of viral release by host / protein K27-linked ubiquitination / 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 / negative regulation of protein deubiquitination / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of type I interferon production ...ISG15 transferase activity / ISG15-protein conjugation / suppression of viral release by host / protein K27-linked ubiquitination / 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 / negative regulation of protein deubiquitination / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of type I interferon production / Phosphorylation of the APC/C / negative regulation of viral transcription / protein K6-linked ubiquitination / (E3-independent) E2 ubiquitin-conjugating enzyme / cellular response to chemical stress / STING mediated induction of host immune responses / E2 ubiquitin-conjugating enzyme / stress granule disassembly / pyroptotic inflammatory response / negative regulation of NF-kappaB transcription factor activity / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / response to type II interferon / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / proteasomal protein catabolic process / protein K48-linked ubiquitination / protein autoubiquitination / positive regulation of cell cycle / positive regulation of autophagy / antiviral innate immune response / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Regulation of innate immune responses to cytosolic DNA / autophagosome / negative regulation of innate immune response / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / positive regulation of DNA-binding transcription factor activity / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / P-body / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / protein destabilization / RING-type E3 ubiquitin transferase / CDK-mediated phosphorylation and removal of Cdc6 / ISG15 antiviral mechanism / protein polyubiquitination / cytoplasmic stress granule / Interferon gamma signaling / ubiquitin-protein transferase activity / Separation of Sister Chromatids / positive regulation of protein binding / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / transcription coactivator activity / positive regulation of viral entry into host cell / protein ubiquitination / ribonucleoprotein complex / innate immune response / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
zinc finger of C3HC4-type, RING / TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / Modified RING finger domain / U-box domain / : / SPRY-associated domain / SPRY-associated / PRY / Ubiquitin Conjugating Enzyme ...zinc finger of C3HC4-type, RING / TRIM21, PRY/SPRY domain / Zinc finger, B-box, chordata / Modified RING finger domain / U-box domain / : / SPRY-associated domain / SPRY-associated / PRY / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Butyrophylin-like, SPRY 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) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / 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 / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase TRIM21 / Ubiquitin-conjugating enzyme E2 E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.82 Å
AuthorsAnandapadamanaban, M. / Moche, M. / Sunnerhagen, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J.Biol.Chem. / Year: 2019
Title: E3 ubiquitin-protein ligase TRIM21-mediated lysine capture by UBE2E1 reveals substrate-targeting mode of a ubiquitin-conjugating E2.
Authors: Anandapadamanaban, M. / Kyriakidis, N.C. / Csizmok, V. / Wallenhammar, A. / Espinosa, A.C. / Ahlner, A. / Round, A.R. / Trewhella, J. / Moche, M. / Wahren-Herlenius, M. / Sunnerhagen, M.
History
DepositionJan 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / 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 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase TRIM21
B: E3 ubiquitin-protein ligase TRIM21
C: E3 ubiquitin-protein ligase TRIM21
D: E3 ubiquitin-protein ligase TRIM21
E: E3 ubiquitin-protein ligase TRIM21
F: E3 ubiquitin-protein ligase TRIM21
G: E3 ubiquitin-protein ligase TRIM21
H: E3 ubiquitin-protein ligase TRIM21
I: Ubiquitin-conjugating enzyme E2 E1
J: Ubiquitin-conjugating enzyme E2 E1
K: Ubiquitin-conjugating enzyme E2 E1
L: Ubiquitin-conjugating enzyme E2 E1
M: Ubiquitin-conjugating enzyme E2 E1
N: Ubiquitin-conjugating enzyme E2 E1
O: Ubiquitin-conjugating enzyme E2 E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,16435
Polymers212,74915
Non-polymers1,41520
Water1,964109
1
A: E3 ubiquitin-protein ligase TRIM21
E: E3 ubiquitin-protein ligase TRIM21
K: Ubiquitin-conjugating enzyme E2 E1
N: Ubiquitin-conjugating enzyme E2 E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9469
Polymers57,5924
Non-polymers3545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase TRIM21
C: E3 ubiquitin-protein ligase TRIM21
M: Ubiquitin-conjugating enzyme E2 E1
O: Ubiquitin-conjugating enzyme E2 E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8548
Polymers57,5924
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: E3 ubiquitin-protein ligase TRIM21
F: E3 ubiquitin-protein ligase TRIM21
I: Ubiquitin-conjugating enzyme E2 E1
L: Ubiquitin-conjugating enzyme E2 E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,03810
Polymers57,5924
Non-polymers4466
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: E3 ubiquitin-protein ligase TRIM21
H: E3 ubiquitin-protein ligase TRIM21
J: Ubiquitin-conjugating enzyme E2 E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3278
Polymers39,9733
Non-polymers3545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.835, 95.871, 235.097
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: 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: 11176.859 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM21, RNF81, RO52, SSA1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Ros-2
References: UniProt: P19474, RING-type E3 ubiquitin transferase
#2: Protein
Ubiquitin-conjugating enzyme E2 E1 / (E3-independent) E2 ubiquitin-conjugating enzyme E1 / E2 ubiquitin-conjugating enzyme E1 / UbcH6 / ...(E3-independent) E2 ubiquitin-conjugating enzyme E1 / E2 ubiquitin-conjugating enzyme E1 / UbcH6 / Ubiquitin carrier protein E1 / Ubiquitin-protein ligase E1


Mass: 17619.188 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2E1, UBCH6 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Ros-2
References: UniProt: P51965, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100mM Bicine pH 9.0 and 5% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.278383 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 28, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.278383 Å / Relative weight: 1
ReflectionResolution: 2.82→47.9 Å / Num. obs: 51064 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.81 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Net I/σ(I): 17
Reflection shellResolution: 2.82→2.912 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2694 / CC1/2: 0.705 / Rpim(I) all: 0.42 / Rrim(I) all: 1.13 / % possible all: 50.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
STARANISOdata scaling
SHELXCDphasing
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.82→47.9 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.887 / SU B: 25.399 / SU ML: 0.455 / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29407 2549 5 %RANDOM
Rwork0.25283 ---
obs0.25492 48491 91.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 90.688 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å2-0 Å2-0.56 Å2
2--0.54 Å2-0 Å2
3----1.37 Å2
Refinement stepCycle: 1 / Resolution: 2.82→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13057 0 40 109 13206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01313374
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712441
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.6518157
X-RAY DIFFRACTIONr_angle_other_deg1.3091.57229027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.41351652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37821.963657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.144152304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8361594
X-RAY DIFFRACTIONr_chiral_restr0.0670.21793
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022672
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.4839.6156653
X-RAY DIFFRACTIONr_mcbond_other6.4799.6156652
X-RAY DIFFRACTIONr_mcangle_it10.45514.3988290
X-RAY DIFFRACTIONr_mcangle_other10.45414.3988291
X-RAY DIFFRACTIONr_scbond_it5.68110.0056721
X-RAY DIFFRACTIONr_scbond_other5.68110.0056722
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.50414.8049868
X-RAY DIFFRACTIONr_long_range_B_refined18.30153425
X-RAY DIFFRACTIONr_long_range_B_other18.29953411
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.816→2.889 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 99 -
Rwork0.365 1802 -
obs--47.12 %

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