7OW2: E3 RING ligase binding domain with peptide

E3 RING ligase binding domain with peptide. Determined by X-ray diffraction at 2.17 Å resolution. Released 13 Jul 2022.

Method: X-ray diffraction
Resolution: 2.17 Å
Organism: Homo sapiens
Chains: 8
Atoms: 5,754
Mol. weight: 80.43 kDa
Ligands: PO4
Released: 13 Jul 2022

Explore 7OW2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7OW2 contains 9 α-helices and 64 β-strands across 8 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: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	14-16	3	2
β-strand	22-25	4	2
β-strand	44-46	3	3
β-strand	47	1	1
β-strand	51	1	3
β-strand	55-62	8	2
β-strand	68-74	7	3
α-helix	82-84	3
α-helix	87-89	3
β-strand	91-97	7	3
β-strand	100-103	4	3
β-strand	110-111	2	3
β-strand	119-125	7	2
β-strand	130-135	6	2
α-helix	136-138	3
β-strand	140-146	7	2
β-strand	153-159	7	3
β-strand	166-169	4	2

Chain B: 0 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	4
β-strand	14-16	3	5
β-strand	22-25	4	5
β-strand	44-46	3	6
β-strand	47	1	4
β-strand	51	1	6
β-strand	55-62	8	5
β-strand	68-74	7	6
β-strand	91-97	7	6
β-strand	100-103	4	6
β-strand	110-111	2	6
β-strand	119-125	7	5
β-strand	130-135	6	5
β-strand	140-146	7	5
β-strand	153-159	7	6
β-strand	166-169	4	5

Chain C: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	14-16	3	8
α-helix	17	1
β-strand	22-25	4	8
β-strand	44-46	3	9
β-strand	47	1	7
β-strand	51	1	9
β-strand	55-62	8	8
β-strand	68-74	7	9
β-strand	91-97	7	9
β-strand	100-103	4	9
β-strand	110-111	2	9
β-strand	119-125	7	8
β-strand	130-135	6	8
β-strand	140-146	7	8
β-strand	153-159	7	9
β-strand	166-169	4	8

Chain D: 1 helix, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	10
β-strand	14-16	3	11
β-strand	22-25	4	11
β-strand	44-46	3	12
β-strand	47	1	10
β-strand	51	1	12
β-strand	55-62	8	11
β-strand	68-74	7	12
β-strand	91-97	7	12
β-strand	100-103	4	12
β-strand	110-111	2	12
β-strand	119-125	7	11
β-strand	130-135	6	11
α-helix	136-138	3
β-strand	140-146	7	11
β-strand	153-159	7	12
β-strand	166-169	4	11

Chains E, F, G and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	20-24	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase TRIM7	A, B, C, D	protein	171	Homo sapiens	Q9C029 (AlphaFold model)
E3 ubiquitin-protein ligase RNF187 peptide	E, F, G, H	protein	7	Homo sapiens	Q5TA31 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>7OW2_1 E3 ubiquitin-protein ligase TRIM7 (chains A, B, C, D)
MVELTLDPDTANPRLILSLDLKGVRLGERAQDLPNHPCRFDTNTRVLASCGFSSGRHHWE
VEVGSKDGWAFGVARESVRRKGLTPFTPEEGVWALQLNGGQYWAVTSPERSPLSCGHLSR
VRVALDLEVGAVSFYAVEDMRHLYTFRVNFQERVFPLFSVCSTGTYLRIWP

Sequence of entity 2 (E, F, G, H), FASTA

>7OW2_2 E3 ubiquitin-protein ligase RNF187 peptide (chains E, F, G, H)
GLSMLLQ

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

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

Primary citation

E3 ligase targeting domain. James, L.C. To be published.

Other PDB entries of the same protein (UniProt Q9C029 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7W0Q 1.1 Å, TRIM7 in complex with C-terminal peptide of 2C
7X70 1.25 Å, TRIM7 in complex with C-terminal peptide of NSP8
7X6Y 1.39 Å, TRIM7 in complex with C-terminal peptide of NSP5
7W0S 1.4 Å, TRIM7 in complex with C-terminal peptide of 2C
7X6Z 1.43 Å, TRIM7 in complex with C-terminal peptide of NSP12
9HIN 1.55 Å, Crystal structure of human TRIM7 PRYSPRY domain bound to…
7W0T 1.57 Å, TRIM7 in complex with C-terminal peptide of 2C
6UMA 1.6 Å, Crystal structure of the TRIM7 B30.2 domain at 1.6 angstrom resolution
8R5B 1.6 Å, Crystal structure of human TRIM7 PRYSPRY domain bound to (3-phenoxybenzoyl)-L-glutamine
8R5C 1.6 Å, Crystal structure of human TRIM7 PRYSPRY domain bound to…
8A5L 1.62 Å, TRIM7 PRYSPRY in complex with a 2BC peptide TIEALFQ
7OVX 1.7 Å, E3 RING ligase binding domain

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