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- PDB-4tkp: Complex of Ubc13 with the RING domain of the TRIM5alpha retrovira... -

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Basic information

Entry
Database: PDB / ID: 4tkp
TitleComplex of Ubc13 with the RING domain of the TRIM5alpha retroviral restriction factor
Components
  • Tripartite motif-containing protein 5
  • Ubiquitin-conjugating enzyme E2 N
KeywordsLIGASE / HIV restriction / TRIM5 / Ubc13 / E3 Ubiquitin ligase / RING dimerization
Function / homology
Function and homology information


: / UBC13-MMS2 complex / regulation of viral entry into host cell / ubiquitin conjugating enzyme complex / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / negative regulation of viral entry into host cell ...: / UBC13-MMS2 complex / regulation of viral entry into host cell / ubiquitin conjugating enzyme complex / regulation of lipopolysaccharide-mediated signaling pathway / suppression of viral release by host / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / negative regulation of viral entry into host cell / negative regulation of viral transcription / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction / pattern recognition receptor activity / E2 ubiquitin-conjugating enzyme / negative regulation of viral genome replication / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / antiviral innate immune response / regulation of DNA repair / positive regulation of autophagy / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / negative regulation of TORC1 signaling / positive regulation of DNA repair / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / activation of innate immune response / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / ubiquitin binding / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / P-body / NOD1/2 Signaling Pathway / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / autophagy / positive regulation of DNA-binding transcription factor activity / Formation of Incision Complex in GG-NER / FCERI mediated NF-kB activation / Aggrephagy / Interleukin-1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / regulation of protein localization / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / Processing of DNA double-strand break ends / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / positive regulation of MAPK cascade / protein ubiquitination / innate immune response / ubiquitin protein ligase binding / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / protein-containing complex / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site ...Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / 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. / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 N / Tripartite motif-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsJohnson, R. / Taylor, A.B. / Hart, P.J. / Ivanov, D.N.
CitationJournal: Cell Rep / Year: 2015
Title: RING Dimerization Links Higher-Order Assembly of TRIM5 alpha to Synthesis of K63-Linked Polyubiquitin.
Authors: Yudina, Z. / Roa, A. / Johnson, R. / Biris, N. / de Souza Aranha Vieira, D.A. / Tsiperson, V. / Reszka, N. / Taylor, A.B. / Hart, P.J. / Demeler, B. / Diaz-Griffero, F. / Ivanov, D.N.
History
DepositionMay 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 N
B: Tripartite motif-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7745
Polymers27,5472
Non-polymers2273
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-9 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.170, 78.170, 82.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / Ubc13 / UbcH13 / Ubiquitin carrier protein N / ...Bendless-like ubiquitin-conjugating enzyme / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17184.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Plasmid: pET30a, modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta 2 / References: UniProt: P61088, ubiquitin-protein ligase
#2: Protein Tripartite motif-containing protein 5 / TRIM5alpha


Mass: 10361.955 Da / Num. of mol.: 1 / Fragment: UNP residues 2-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: TRIM5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q0PF16, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2.0 M ammonium sulfate, 0.1 M bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2823 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2823 Å / Relative weight: 1
ReflectionResolution: 2.08→45.93 Å / Num. obs: 15907 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 50.9 Å2 / Rsym value: 0.036 / Net I/σ(I): 23.9
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.08→45.93 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 778 5.04 %random
Rwork0.2243 ---
obs0.2257 15568 97.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.6 Å2
Refinement stepCycle: LAST / Resolution: 2.08→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 7 49 1712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021696
X-RAY DIFFRACTIONf_angle_d0.6642306
X-RAY DIFFRACTIONf_dihedral_angle_d16.252647
X-RAY DIFFRACTIONf_chiral_restr0.047263
X-RAY DIFFRACTIONf_plane_restr0.003298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.15440.33351550.32512751X-RAY DIFFRACTION99
2.1544-2.24060.31961640.30052633X-RAY DIFFRACTION95
2.2406-2.34260.38111450.35032595X-RAY DIFFRACTION94
2.3426-2.46610.27731440.25662775X-RAY DIFFRACTION99
2.4661-2.62060.32531490.2432759X-RAY DIFFRACTION100
2.6206-2.82290.33651270.25292803X-RAY DIFFRACTION99
2.8229-3.10690.30341570.24942759X-RAY DIFFRACTION99
3.1069-3.55640.26491590.22662756X-RAY DIFFRACTION99
3.5564-4.48010.22811010.19212766X-RAY DIFFRACTION98
4.4801-45.94240.20761500.2052724X-RAY DIFFRACTION98

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