5VNZ | pdb_00005vnz

Structure of a TRAF6-Ubc13~Ub complex

PDB DOI: https://doi.org/10.2210/pdb5VNZ/pdb

Classification: TRANSFERASE
Organism(s): Danio rerio, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-05-01 Released: 2017-12-06
Deposition Author(s): Middleton, A.J., Day, C.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.41 Å
R-Value Free:
0.294 (Depositor), 0.290 (DCC)
R-Value Work:
0.237 (Depositor), 0.236 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The activity of TRAF RING homo- and heterodimers is regulated by zinc finger 1.

Middleton, A.J., Budhidarmo, R., Das, A., Zhu, J., Foglizzo, M., Mace, P.D., Day, C.L.

(2017) Nat Commun 8: 1788-1788

PubMed: 29176576 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-017-01665-3
Primary Citation Related Structures:
5VNZ, 5VO0

PubMed Abstract:
Ubiquitin chains linked through lysine63 (K63) play a critical role in inflammatory signalling. Following ligand engagement of immune receptors, the RING E3 ligase TRAF6 builds K63-linked chains together with the heterodimeric E2 enzyme Ubc13-Uev1A. Dimerisation of the TRAF6 RING domain is essential for the assembly of K63-linked ubiquitin chains. Here, we show that TRAF6 RING dimers form a catalytic complex where one RING interacts with a Ubc13~Ubiquitin conjugate, while the zinc finger 1 (ZF1) domain and linker-helix of the opposing monomer contact ubiquitin. The RING dimer interface is conserved across TRAFs and we also show that TRAF5-TRAF6 heterodimers form. Importantly, TRAF5 can provide ZF1, enabling ubiquitin transfer from a TRAF6-bound Ubc13 conjugate. Our study explains the dependence of activity on TRAF RING dimers, and suggests that both homo- and heterodimers mediated by TRAF RING domains have the capacity to synthesise ubiquitin chains.

Organizational Affiliation

Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand.

Macromolecule Content

Total Structure Weight: 80.1 kDa
Atom Count: 5,327
Modeled Residue Count: 668
Deposited Residue Count: 702
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TNF receptor-associated factor 6	A, D	118	Danio rerio	Mutation(s): 0 Gene Names: traf6, si:dkey-56p7.3, zgc:63704 EC: 2.3.2.27
UniProt
Find proteins for Q6IWL4 (Danio rerio) Explore Q6IWL4 Go to UniProtKB: Q6IWL4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6IWL4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 N	B, E	157	Homo sapiens	Mutation(s): 3 Gene Names: UBE2N, BLU EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens) Explore P61088 Go to UniProtKB: P61088
PHAROS: P61088 GTEx: ENSG00000177889
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61088
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C, F	76	Homo sapiens	Mutation(s): 0 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47 GTEx: ENSG00000170315
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	G [auth A] H [auth A] I [auth A] J [auth D] K [auth D] G [auth A], H [auth A], I [auth A], J [auth D], K [auth D], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.41 Å
R-Value Free: 0.294 (Depositor), 0.290 (DCC)
R-Value Work: 0.237 (Depositor), 0.236 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.36	α = 90
b = 170.551	β = 90
c = 97.312	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-12-06

Deposition Author(s):

Middleton, A.J.

Day, C.L.

Revision History (Full details and data files)

Version 1.0: 2017-12-06
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary