7Q43: RCC1-Like domain 2 of ubiquitin ligase HERC2

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Nov 2022.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,934
Mol. weight: 137 kDa
Ligands: CIT
Released: 16 Nov 2022

Explore 7Q43 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Q43 contains 34 α-helices and 84 β-strands across 3 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: 12 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2961-2966	6	8
β-strand	2979-2985	7	8
α-helix	2987-2991	5
β-strand	2994-3000	7	9
β-strand	3003-3008	6	9
β-strand	3013-3018	6	9
α-helix	3020-3022	3
β-strand	3032-3038	7	9
α-helix	3040-3042	3
β-strand	3047-3052	6	10
β-strand	3058-3063	6	10
β-strand	3068-3072	5	10
α-helix	3075-3077	3
β-strand	3087-3092	6	10
α-helix	3094-3096	3
β-strand	3101-3106	6	11
β-strand	3110-3115	6	11
β-strand	3120-3124	5	11
α-helix	3127-3129	3
β-strand	3139-3144	6	11
α-helix	3146-3148	3
β-strand	3153-3158	6	12
β-strand	3164-3169	6	12
β-strand	3174-3178	5	12
α-helix	3181-3183	3
β-strand	3193-3198	6	12
α-helix	3200-3202	3
β-strand	3207-3212	6	13
β-strand	3216-3221	6	13
β-strand	3226-3230	5	13
α-helix	3233-3235	3
β-strand	3245-3250	6	13
α-helix	3252-3254	3
β-strand	3259-3264	6	14
β-strand	3268-3273	6	14
β-strand	3278-3282	5	14
β-strand	3297-3302	6	14
α-helix	3303	1
β-strand	3313-3316	4	8
β-strand	3320-3324	5	8

Chain C: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2961-2966	6	1
β-strand	2979-2985	7	1
α-helix	2987-2990	4
β-strand	2994-3000	7	2
β-strand	3003-3008	6	2
β-strand	3013-3018	6	2
α-helix	3020-3022	3
β-strand	3032-3038	7	2
α-helix	3040-3042	3
β-strand	3047-3051	5	3
β-strand	3058-3063	6	3
β-strand	3068-3072	5	3
α-helix	3075-3077	3
β-strand	3087-3092	6	3
α-helix	3094-3096	3
β-strand	3101-3106	6	4
β-strand	3110-3115	6	4
β-strand	3120-3124	5	4
α-helix	3127-3129	3
β-strand	3139-3144	6	4
α-helix	3146-3148	3
β-strand	3153-3158	6	5
β-strand	3164-3169	6	5
β-strand	3174-3178	5	5
α-helix	3181-3183	3
β-strand	3193-3198	6	5
α-helix	3200-3202	3
β-strand	3207-3212	6	6
β-strand	3216-3221	6	6
β-strand	3226-3230	5	6
β-strand	3245-3250	6	6
α-helix	3252-3254	3
β-strand	3259-3264	6	7
β-strand	3268-3273	6	7
β-strand	3278-3282	5	7
β-strand	3297-3302	6	7
α-helix	3303	1
β-strand	3313-3316	4	1
β-strand	3320-3324	5	1

Chain E: 11 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2961-2966	6	15
β-strand	2979-2985	7	15
α-helix	2987-2990	4
β-strand	2994-3000	7	16
β-strand	3003-3008	6	16
β-strand	3013-3017	5	16
α-helix	3020-3022	3
β-strand	3037-3038	2	16
α-helix	3040-3042	3
β-strand	3047-3052	6	17
β-strand	3058-3063	6	17
β-strand	3068-3072	5	17
α-helix	3075-3077	3
β-strand	3087-3092	6	17
α-helix	3094-3096	3
β-strand	3101-3106	6	18
β-strand	3110-3115	6	18
β-strand	3120-3124	5	18
α-helix	3127-3129	3
β-strand	3139-3144	6	18
β-strand	3153-3158	6	19
β-strand	3164-3169	6	19
β-strand	3174-3178	5	19
α-helix	3181-3183	3
β-strand	3193-3198	6	19
α-helix	3200-3202	3
β-strand	3207-3212	6	20
β-strand	3216-3221	6	20
β-strand	3226-3230	5	20
α-helix	3233-3235	3
β-strand	3245-3250	6	20
α-helix	3252-3254	3
β-strand	3259-3264	6	21
β-strand	3268-3273	6	21
β-strand	3278-3282	5	21
β-strand	3297-3302	6	21
α-helix	3303	1
β-strand	3313-3316	4	15
β-strand	3320-3324	5	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase HERC2	A, C, E	protein	405	Homo sapiens	O95714
Dedicator of cytokinesis protein 10 peptide	B, D, F	protein	25	Homo sapiens	Q96BY6 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>7Q43_1 E3 ubiquitin-protein ligase HERC2 (chains A, C, E)
GAMGSLIRKKAAGLESAATIRTKVFVWGLNDKDQLGGLKGSKIKVPSFSETLSALNVVQV
AGGSKSLFAVTVEGKVYACGEATNGRLGLGISSGTVPIPRQITALSSYVVKKVAVHSGGR
HATALTVDGKVFSWGEGDDGKLGHFSRMNCDKPRLIEALKTKRIRDIACGSSHSAALTSS
GELYTWGLGEYGRLGHGDNTTQLKPKMVKVLLGHRVIQVACGSRDAQTLALTDEGLVFSW
GDGDFGKLGRGGSEGCNIPQNIERLNGQGVCQIECGAQFSLALTKSGVVWTWGKGDYFRL
GHGSDVHVRKPQVVEGLRGKKIVHVAVGALHCLAVTDSGQVYAWGDNDHGQQGNGTTTVN
RKPTLVQGLEGQKITRVACGSSHSVAWTTVDVATPSVHEPVLFQT

Sequence of entity 2 (B, D, F), FASTA

>7Q43_2 Dedicator of cytokinesis protein 10 peptide (chains B, D, F)
KLPSHSFEIDHEDADKDEDTTSHSS

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1

Primary citation

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of dedicator of cytokinesis protein 10. Demenge, A., Howard, E., Cousido-Siah, A. et al. To be published.

Other PDB entries of the same protein (UniProt O95714), best resolution first:

9L93 1.73 Å, Crystal structure of NCOA4 in complex with HERC2
3KCI 1.8 Å, The third RLD domain of HERC2
9L8Y 1.92 Å, Crystal structure of HERC2
7Q42 1.95 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
7RGW 1.99 Å, Crystal structure of HERC2 DOC domain
6WW3 2.1 Å, Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail
7Q45 2.1 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
7Q44 2.2 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
6WW4 2.25 Å, Crystal structure of HERC2 ZZ domain in complex with histone H3 tail
7Q40 2.35 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2
7Q46 2.46 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…
4L1M 2.6 Å, Structure of the first RCC1-like domain of HERC2

Browse structure collections

About this viewer

MolViewer shows 7Q43 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.