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- PDB-5vo0: Structure of a TRAF6-Ubc13~Ub complex -

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Basic information

Entry
Database: PDB / ID: 5vo0
TitleStructure of a TRAF6-Ubc13~Ub complex
Components
  • TNF receptor-associated factor 6
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 N
KeywordsTRANSFERASE
Function / homology
Function and homology information


p75NTR recruits signalling complexes / Interleukin-1 signaling / NOD1/2 Signaling Pathway / Ovarian tumor domain proteases / Ub-specific processing proteases / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing ...p75NTR recruits signalling complexes / Interleukin-1 signaling / NOD1/2 Signaling Pathway / Ovarian tumor domain proteases / Ub-specific processing proteases / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / tumor necrosis factor receptor binding / non-canonical NF-kappaB signal transduction / postreplication repair / regulation of canonical NF-kappaB signal transduction / symbiont entry into host cell via disruption of host cell glycocalyx / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitin conjugating enzyme activity / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / regulation of DNA repair / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TICAM1, RIP1-mediated IKK complex recruitment / negative regulation of TORC1 signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / lipid droplet / signaling adaptor activity / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / antiviral innate immune response / activated TAK1 mediates p38 MAPK activation / positive regulation of DNA repair / lipopolysaccharide-mediated signaling pathway / ubiquitin binding / double-strand break repair via homologous recombination / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / response to bacterium / Nonhomologous End-Joining (NHEJ) / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / Formation of Incision Complex in GG-NER / positive regulation of NF-kappaB transcription factor activity / G2/M DNA damage checkpoint / FCERI mediated NF-kB activation / RING-type E3 ubiquitin transferase / Interleukin-1 signaling / Aggrephagy / response to virus / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / T cell receptor signaling pathway / Processing of DNA double-strand break ends / cell cortex / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / innate immune response / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / SARS-CoV-2 activates/modulates innate and adaptive immune responses / glutamatergic synapse / protein-containing complex / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
TNF receptor-associated factor 6 / TNF receptor-associated factor 6, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Zinc finger, C3HC4 type (RING finger) / MATH/TRAF domain ...TNF receptor-associated factor 6 / TNF receptor-associated factor 6, MATH domain / TRAF-type zinc finger / TNF receptor-associated factor TRAF, metazoa / : / TRAF/meprin, MATH domain / Zinc finger, TRAF-type / Zinc finger TRAF-type profile. / Zinc finger, C3HC4 type (RING finger) / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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 / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Tail fiber / Ubiquitin-conjugating enzyme E2 N / TNF receptor-associated factor 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.9 Å
AuthorsMiddleton, A.J. / Day, C.L.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden New Zealand
CitationJournal: Nat Commun / Year: 2017
Title: The activity of TRAF RING homo- and heterodimers is regulated by zinc finger 1.
Authors: Middleton, A.J. / Budhidarmo, R. / Das, A. / Zhu, J. / Foglizzo, M. / Mace, P.D. / Day, C.L.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TNF receptor-associated factor 6
B: Ubiquitin-conjugating enzyme E2 N
C: Ubiquitin
D: TNF receptor-associated factor 6
E: Ubiquitin-conjugating enzyme E2 N
F: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,37915
Polymers91,8176
Non-polymers5629
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-103 kcal/mol
Surface area34530 Å2
Unit cell
Length a, b, c (Å)181.114, 181.114, 97.414
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein TNF receptor-associated factor 6 / E3 ubiquitin-protein ligase TRAF6 / RING-type E3 ubiquitin transferase TRAF6


Mass: 19765.547 Da / Num. of mol.: 2 / Fragment: residues 50-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: traf6, si:dkey-56p7.3, zgc:63704 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q6IWL4*PLUS, RING-type E3 ubiquitin transferase
#2: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17566.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#3: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0CG47
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
Has protein modificationY

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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: 4.35 Å3/Da / Density % sol: 75.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100-200 mM Na/K tartrate, 11-15% PEG 3350 and 100 mM bis-Tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.9→128.4 Å / Num. obs: 14890 / % possible obs: 97.9 % / Redundancy: 4.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.091 / Rrim(I) all: 0.208 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.9-4.364.90.7010.8020.340.78298.6
8.72-49.374.60.0460.9970.0230.05295.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimless0.5.27data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HCT

3hct


Resolution: 3.9→128.4 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.815 / SU B: 43.588 / SU ML: 0.592 / Cross valid method: THROUGHOUT / ESU R Free: 0.76 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2992 719 4.8 %RANDOM
Rwork0.2524 ---
obs0.25468 14112 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.268 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å20 Å2
2---0.15 Å2-0 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 3.9→128.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5660 0 9 0 5669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195807
X-RAY DIFFRACTIONr_bond_other_d0.0020.025438
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9837851
X-RAY DIFFRACTIONr_angle_other_deg1.0083.00412669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2324.613271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.917151048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9031541
X-RAY DIFFRACTIONr_chiral_restr0.0740.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216327
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021092
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_it4.07111.0022842
X-RAY DIFFRACTIONr_mcbond_other4.06711.0022841
X-RAY DIFFRACTIONr_mcangle_it7.19716.4873542
X-RAY DIFFRACTIONr_mcangle_other7.19716.4893543
X-RAY DIFFRACTIONr_scbond_it3.63911.4922965
X-RAY DIFFRACTIONr_scbond_other3.63811.4932966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.50117.0374310
X-RAY DIFFRACTIONr_long_range_B_refined15.10121709
X-RAY DIFFRACTIONr_long_range_B_other15.121708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 66 -
Rwork0.362 981 -
obs--95.62 %

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