7ZJ3: TRIM2 RING domain

Name: PDB 7ZJ3: Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate
Published: 2022-11-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate. Determined by X-ray diffraction at 2.53 Å resolution. Released 30 Nov 2022.

Method: X-ray diffraction
Resolution: 2.53 Å
Organism: Homo sapiens
Chains: 12
Atoms: 9,950
Mol. weight: 146.64 kDa
Ligands: ZN
Released: 30 Nov 2022

Explore 7ZJ3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZJ3 contains 63 α-helices and 95 β-strands across 12 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	22	1	25
β-strand	29	1	25
β-strand	33-35	3	26
β-strand	41-43	3	26
α-helix	44-50	7
α-helix	52	1
β-strand	57-59	3	27
β-strand	66-68	3	27
α-helix	69-70	2
α-helix	74-76	3
β-strand	78-79	2	26
α-helix	81-92	12

Chain B: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	1-15	15
β-strand	21-25	5	31
β-strand	32-38	7	31
α-helix	39-40	2
β-strand	49-55	7	31
α-helix	64-65	2
β-strand	66-69	4	31
β-strand	75	1	32
β-strand	78	1	32
β-strand	83	1	31
β-strand	84	1	32
β-strand	86	1	30
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-144	14

Chain C: 2 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	28
β-strand	12-16	5	28
β-strand	22	1	29
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	28
β-strand	48-49	2	28
β-strand	55	1	29
β-strand	66-71	6	28
β-strand	75	1	30

Chain D: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	22	1	1
β-strand	29	1	1
β-strand	33-35	3	2
β-strand	41-43	3	2
α-helix	44-50	7
α-helix	52	1
β-strand	57-59	3	3
β-strand	66-68	3	3
α-helix	69-70	2
α-helix	74-76	3
α-helix	78	1
β-strand	79	1	2
α-helix	81-91	11

Chain E: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	1-15	15
β-strand	21-25	5	4
β-strand	32-38	7	4
α-helix	39-40	2
β-strand	49-55	7	4
β-strand	66-69	4	4
β-strand	75	1	5
β-strand	78	1	5
β-strand	83	1	4
β-strand	84	1	5
β-strand	86	1	6
α-helix	87-89	3
α-helix	99-110	12
α-helix	121-129	9
α-helix	131-144	14

Chain F: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	12-16	5	7
β-strand	22	1	8
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
β-strand	55	1	8
α-helix	57-59	3
β-strand	66-71	6	7
β-strand	75	1	6

Chain G: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	22	1	9
β-strand	29	1	9
β-strand	33-35	3	10
β-strand	41-43	3	10
α-helix	44-50	7
α-helix	52	1
β-strand	57-59	3	11
β-strand	66-68	3	11
α-helix	69-70	2
α-helix	74-76	3
α-helix	78	1
β-strand	79	1	10
α-helix	81-92	12

Chain H: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	-2-0	3
α-helix	1-15	15
β-strand	21-25	5	12
β-strand	32-38	7	12
α-helix	39-40	2
β-strand	49-55	7	12
β-strand	66-69	4	12
β-strand	78	1	13
β-strand	83	1	12
β-strand	84	1	13
β-strand	86	1	14
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-144	14

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tripartite motif-containing protein 2	A, D, G, J	protein	97	Homo sapiens	Q9C040 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 D1	B, E, H, K	protein	150	Homo sapiens	P51668 (AlphaFold model)
Polyubiquitin-C	C, F, I, L	protein	80	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>7ZJ3_1 Tripartite motif-containing protein 2 (chains A, D, G, J)
GPGASEGTNIPSPVVRQIDKQFLICSICLERYKNPKVLPCLHTFCERCLQNYIPAHSLTL
SCPVCRQTSILPEKGVAALQNNFFITNLMDVLQRTPG

Sequence of entity 2 (B, E, H, K), FASTA

>7ZJ3_2 Ubiquitin-conjugating enzyme E2 D1 (chains B, E, H, K)
GPLGSALKRIQKELSDLQRDPPAHCRAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHF
PTDYPFKPPKIAFTTKIYHPNINSNGSIKLDILRSQWSPALTVSKVLLSICSLLCDPNPD
DPLVPDIAQIYKSDKEKYNRHAREWTQKYA

Sequence of entity 3 (C, F, I, L), FASTA

>7ZJ3_3 Polyubiquitin-C (chains C, F, I, L)
GAMGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTL
SDYNIQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Divergent self-association properties of paralogous proteins TRIM2 and TRIM3 regulate their E3 ligase activity. Esposito, D., Dudley-Fraser, J., Garza-Garcia, A. et al. Nat Commun (2022) 13:7583-7583. DOI 10.1038/s41467-022-35300-7 · PubMed

Other PDB entries of the same protein (UniProt Q9C040 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7QRV 1.45 Å, Crystal structure of NHL domain of TRIM2 (full C-terminal)
7B2R 1.6 Å, Crystal structure of NHL domain of TRIM2
7B96 1.8 Å, NHL domain of human TRIM2
8A38 2.2 Å, RING domain of human TRIM2
8AMS 2.4 Å, Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin

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