4TKP: Ubiquitin-conjugating enzyme E2 N

Complex of Ubc13 with the RING domain of the TRIM5alpha retroviral restriction factor. Determined by X-ray diffraction at 2.08 Å resolution. Released 22 Jul 2015.

Method: X-ray diffraction
Resolution: 2.08 Å
Organisms: Homo sapiens, Macaca mulatta
Chains: 2
Atoms: 1,712
Mol. weight: 27.77 kDa
Ligands: ZN
Released: 22 Jul 2015

Explore 4TKP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4TKP contains 11 α-helices and 12 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	19-20	2
β-strand	23-27	5	1
β-strand	34-40	7	1
α-helix	41-42	2
β-strand	51-57	7	1
α-helix	66-67	2
β-strand	68-71	4	1
β-strand	77	1	2
β-strand	80	1	2
β-strand	86	1	2
α-helix	89-91	3
α-helix	101-113	13
α-helix	124-131	8
α-helix	133-147	15

Chain B: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	14	1	3
β-strand	21	1	3
β-strand	25-27	3	4
β-strand	33-35	3	4
α-helix	36-38	3
β-strand	69-70	2	4
α-helix	72-79	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 N	A	protein	153	Homo sapiens	P61088 (AlphaFold model)
Tripartite motif-containing protein 5	B	protein	93	Macaca mulatta	Q0PF16 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4TKP_1 Ubiquitin-conjugating enzyme E2 N (chains A)
GTAGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLP
EEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDD
PLANDVAEQWKTNEAQAIETARAWTRLYAMNNI

Sequence of entity 2 (B), FASTA

>4TKP_2 Tripartite motif-containing protein 5 (chains B)
GSASGILLNVKEEVTCPICLELLTEPLSLHCGHSFCQACITANHKKSMLYKEGERSCPVC
RISYQPENIQPNRHVANIVEKLREVKLSPEEGQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

RING Dimerization Links Higher-Order Assembly of TRIM5 alpha to Synthesis of K63-Linked Polyubiquitin. Yudina, Z., Roa, A., Johnson, R. et al. Cell Rep (2015) 12:788-797. DOI 10.1016/j.celrep.2015.06.072 · PubMed

Other PDB entries of the same protein (UniProt P61088 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4ONL 1.35 Å, Crystal structure of human Mms2/Ubc13_D81N, R85S, A122V, N123P
4ONM 1.35 Å, Crystal structure of human Mms2/Ubc13 - NSC697923
5YWR 1.47 Å, Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13)
4ONN 1.5 Å, Crystal structure of human Mms2/Ubc13 - BAY 11-7082
9BIV 1.68 Å, Crystal Structure of Ubc13 with a New Active Site Loop Conformation
9LHJ 1.68 Å, UBE2N/UBE2V2 complexed with a covalent inhibitor
4DHI 1.8 Å, Structure of C. elegans OTUB1 bound to human UBC13
4NR3 1.8 Å, Crystal Structure of a human Mms2/Ubc13 L121G mutant
1J7D 1.85 Å, Crystal Structure of hMms2-hUbc13
4NRG 1.95 Å, Crystal Structure of a human Mms2/Ubc13 D118G mutant
6ULH 1.97 Å, Structure of MavC in complex with its substrate in R3 spacegroup
6P5B 2.1 Å, Crystal Structure of MavC in Complex with Ub-UbE2N

Browse structure collections

About this viewer

MolViewer shows 4TKP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.