7Q41: 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 ubiquitin-protein ligase E3A (E6AP). Determined by X-ray diffraction at 3.01 Å resolution. Released 16 Nov 2022.

Method: X-ray diffraction
Resolution: 3.01 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,504
Mol. weight: 133.87 kDa
Ligands: CIT
Released: 16 Nov 2022

Explore 7Q41 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Q41 contains 36 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	1
β-strand	2979-2985	7	1
α-helix	2987-2992	6
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	3047-3052	6	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
α-helix	3233-3235	3
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

Chains C and E: 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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-protein ligase E3A (E6AP) peptide	B, D, F	protein	15	Homo sapiens	Q05086 (AlphaFold model)
E3 ubiquitin-protein ligase HERC2	A, C, E	protein	405	Homo sapiens	O95714

Sequence of entity 1 (B, D, F), FASTA

>7Q41_1 Ubiquitin-protein ligase E3A (E6AP) peptide (chains B, D, F)
AKDEDKDEDEKEKAA

Sequence of entity 2 (A, C, E), FASTA

>7Q41_2 E3 ubiquitin-protein ligase HERC2 (chains A, C, E)
GAMGSLIRKKAAGLESAATIRTKVFVWGLNDKDQLGGLKGSKIKVPSFSETLSALNVVQV
AGGSKSLFAVTVEGKVYACGEATNGRLGLGISSGTVPIPRQITALSSYVVKKVAVHSGGR
HATALTVDGKVFSWGEGDDGKLGHFSRMNCDKPRLIEALKTKRIRDIACGSSHSAALTSS
GELYTWGLGEYGRLGHGDNTTQLKPKMVKVLLGHRVIQVACGSRDAQTLALTDEGLVFSW
GDGDFGKLGRGGSEGCNIPQNIERLNGQGVCQIECGAQFSLALTKSGVVWTWGKGDYFRL
GHGSDVHVRKPQVVEGLRGKKIVHVAVGALHCLAVTDSGQVYAWGDNDHGQQGNGTTTVN
RKPTLVQGLEGQKITRVACGSSHSVAWTTVDVATPSVHEPVLFQT

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	2

Primary citation

Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with DXDKDED motif of ubiquitin-protein ligase E3A (E6AP). Demenge, A., Howard, E., Cousido-Siah, A. et al. To be published.

Other PDB entries of the same protein (UniProt Q05086 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TGK 1.3 Å, Domain swapped E6AP C-lobe dimer
6SJV 2.03 Å, Structure of HPV18 E6 oncoprotein in complex with mutant E6AP LxxLL motif
4XR8 2.25 Å, Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution
7QPB 2.34 Å, Catalytic C-lobe of the HECT-type ubiquitin ligase E6AP in complex with a hybrid…
4GIZ 2.55 Å, Crystal structure of full-length human papillomavirus oncoprotein E6 in complex with…
9L3L 2.59 Å, Crystal structure of the C lobe of E6AP in complex with K48-linked diUb
1C4Z 2.6 Å, Structure of an E6AP-UBCH7 complex: insights into the ubiquitination pathway
8JRN 2.6 Å, Structure of E6AP-E6 complex in Att1 state
1D5F 2.8 Å, Structure of E6AP: insights into ubiquitination pathway
6SLM 2.8 Å, Crystal structure of full-length HPV31 E6 oncoprotein in complex with LXXLL peptide of…
8JRO 3.01 Å, Structure of E6AP-E6 complex in Att2 state
9U4A 3.3 Å, Structure of UBE3A T485E tetramer

Browse structure collections

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