8AMS: Ubiquitin-conjugating enzyme E2 D3

Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin. Determined by X-ray diffraction at 2.4 Å resolution. Released 15 Nov 2023.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 5
Atoms: 4,389
Mol. weight: 80.84 kDa
Ligands: PE8, ZN
Released: 15 Nov 2023

Explore 8AMS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AMS contains 28 α-helices and 37 β-strands across 5 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	1-15	15
β-strand	21-25	5	1
β-strand	32-38	7	1
α-helix	39-40	2
β-strand	49-55	7	1
β-strand	66-69	4	1
β-strand	75	1	2
β-strand	78	1	2
β-strand	83	1	1
β-strand	84	1	2
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-127	7
α-helix	131-145	15

Chain B: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	0-15	16
β-strand	21-25	5	3
β-strand	32-38	7	3
α-helix	39-40	2
β-strand	49-55	7	3
β-strand	66-69	4	3
β-strand	75	1	4
β-strand	78	1	4
β-strand	83	1	3
β-strand	84	1	4
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain C: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	22	1	5
β-strand	29	1	5
β-strand	33-35	3	6
β-strand	41-43	3	6
α-helix	44-50	7
β-strand	57-59	3	7
β-strand	66-68	3	7
α-helix	69-70	2
α-helix	74-76	3
α-helix	78	1
β-strand	79	1	6
α-helix	81-91	11

Chain D: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	22	1	8
β-strand	29	1	8
β-strand	34-35	2	9
β-strand	41-42	2	9
α-helix	44-50	7
β-strand	57-59	3	10
β-strand	66-68	3	10
α-helix	69-70	2
α-helix	74-76	3
α-helix	78	1
β-strand	79	1	9
α-helix	81-89	9

Chain E: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	11
β-strand	12-17	6	11
β-strand	22	1	12
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	11
β-strand	48-49	2	11
α-helix	50-51	2
β-strand	55	1	12
α-helix	57-59	3
β-strand	66-71	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-conjugating enzyme E2 D3	A, B	protein	149	Homo sapiens	P61077 (AlphaFold model)
Tripartite motif-containing protein 2	C, D	protein	153	Homo sapiens	Q9C040 (AlphaFold model)
Polyubiquitin-C	E	protein	101	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8AMS_1 Ubiquitin-conjugating enzyme E2 D3 (chains A, B)
GHMALKRINKELSDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPT
DYPFKPPKVAFTTRIYHPNINSNGSISLDILRSQWSPALTISKVLLSICSLLCDPNPDDP
LVPEIARIYKTDRDKYNRISREWTQKYAM

Sequence of entity 2 (C, D), FASTA

>8AMS_2 Tripartite motif-containing protein 2 (chains C, D)
GAMIPSPVVRQIDKQFLICSICLERYKNPKVLPCLHTFCERCLQNYIPAHSLTLSCPVCR
QTSILPEKGVAALQNNFFITNLMDVLQRTPGSNAEESSILETVTAVAAGKPLSCPNHDGN
VMEFYCQSCETAMCRECTEGEHAEHPTVPLKDV

Sequence of entity 3 (E), FASTA

>8AMS_3 Polyubiquitin-C (chains E)
MKHHHHHHPMSDYDIPTTENLYFQGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEG
IPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
PE8	3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol	C16 H34 O9	1
ZN	Zinc ion	Zn	4

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

Primary citation

Structural and biophysical studies of TRIM2 and TRIM3. Perez-Borrajero, C., Hennig, J. To be published.

Other PDB entries of the same protein (UniProt P61077 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EGG 1.76 Å, Crystal structure of human ubiquitin-conjugating enzyme UBCH5C
1X23 1.85 Å, Crystal structure of ubch5c
4S3O 2.0 Å, PCGF5-RING1B-UbcH5c complex
8UQA 2.05 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 12-residue linker
5IFR 2.2 Å, Structure of the stable UBE2D3-UbDha conjugate
8UQ9 2.3 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 4-residue linker
8UQ8 2.34 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 2-residue linker
3UGB 2.35 Å, UbcH5c~Ubiquitin Conjugate
8UQB 2.48 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
6T7F 2.58 Å, RCR E3 ligase E2-Ubiquitin transthiolation intermediate
8UQC 2.61 Å, Crystal structure of RNF168 (RING)-UbcH5c fused to H2A-H2B via a 20-residue linker…
3RPG 2.65 Å, Bmi1/Ring1b-UbcH5c complex structure

Browse structure collections

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