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

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Basic information

Entry
Database: PDB / ID: 5vnz
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 / hypothalamus gonadotrophin-releasing hormone neuron development / DNA damage tolerance / regulation of canonical NF-kappaB signal transduction / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / E2 ubiquitin-conjugating enzyme / female gonad development / positive regulation of double-strand break repair / seminiferous tubule development / ubiquitin conjugating enzyme activity / male meiosis I / positive regulation of intracellular signal transduction / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / regulation of DNA repair / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / lipid droplet / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / signaling adaptor activity / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / antiviral innate immune response / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / lipopolysaccharide-mediated signaling pathway / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / positive regulation of DNA repair / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / ubiquitin binding / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / positive regulation of protein ubiquitination / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential
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 / 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. / Herpes Virus-1 / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / 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 / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / 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: 3.41 Å
AuthorsMiddleton, A.J. / Day, C.L.
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 / struct_ncs_dom_lim
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 / _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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)80,09812
Polymers79,7056
Non-polymers3926
Water00
1
A: TNF receptor-associated factor 6
B: Ubiquitin-conjugating enzyme E2 N
C: Ubiquitin
hetero molecules

A: TNF receptor-associated factor 6
B: Ubiquitin-conjugating enzyme E2 N
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,09812
Polymers79,7056
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
2
D: TNF receptor-associated factor 6
E: Ubiquitin-conjugating enzyme E2 N
F: Ubiquitin
hetero molecules

D: TNF receptor-associated factor 6
E: Ubiquitin-conjugating enzyme E2 N
F: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,09812
Polymers79,7056
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)138.360, 170.551, 97.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPALAALAAA53 - 1594 - 110
21ASPASPALAALADD53 - 1594 - 110
12GLYGLYMETMETBB3 - 1498 - 154
22GLYGLYMETMETEE3 - 1498 - 154
13METMETGLYGLYCC1 - 761 - 76
23METMETGLYGLYFF1 - 761 - 76

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 13709.656 Da / Num. of mol.: 2 / Fragment: residues 50-159
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)
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)
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) / References: UniProt: P0CG47
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
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: 3.59 Å3/Da / Density % sol: 65.76 %
Crystal growTemperature: 289 K / Method: microbatch
Details: 0.05-0.3 mM sodium citrate, 100 mM bBis-Tris propane, and 17-23% PEG 3350

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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: 3.41→107.45 Å / Num. obs: 16046 / % possible obs: 99.6 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.052 / Rrim(I) all: 0.139 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.41-3.687.11.5450.640.6151.66598.3
9.02-48.666.30.0460.9960.020.0598.9

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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: 3.41→107.45 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.881 / SU B: 34.845 / SU ML: 0.505 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.604
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2944 788 4.9 %RANDOM
Rwork0.2369 ---
obs0.2395 15243 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 245.82 Å2 / Biso mean: 155.826 Å2 / Biso min: 106.28 Å2
Baniso -1Baniso -2Baniso -3
1-7.08 Å2-0 Å20 Å2
2--1.58 Å20 Å2
3----8.66 Å2
Refinement stepCycle: final / Resolution: 3.41→107.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5321 0 6 0 5327
Biso mean--131.55 --
Num. residues----668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195449
X-RAY DIFFRACTIONr_bond_other_d0.0010.025140
X-RAY DIFFRACTIONr_angle_refined_deg1.0861.9857365
X-RAY DIFFRACTIONr_angle_other_deg0.8593.00311969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.935662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0324.609256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03215993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0671540
X-RAY DIFFRACTIONr_chiral_restr0.0620.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215936
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021026
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A61700.06
12D61700.06
21B87740.07
22E87740.07
31C43800.04
32F43800.04
LS refinement shellResolution: 3.408→3.496 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 56 -
Rwork0.41 1066 -
all-1122 -
obs--95.08 %

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