4LCD: E3 ubiquitin-protein ligase RSP5

Structure of an Rsp5xUbxSna3 complex: Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3. Determined by X-ray diffraction at 3.1 Å resolution. Released 14 Aug 2013.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Saccharomyces cerevisiae, Homo sapiens
Chains: 6
Atoms: 7,944
Mol. weight: 125.23 kDa
Released: 14 Aug 2013

Explore 4LCD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LCD contains 62 α-helices and 56 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: 29 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	388-390	3
β-strand	393-396	4	1
β-strand	404-407	4	1
β-strand	412-414	3	1
α-helix	421-425	5
α-helix	430-442	13
α-helix	446-448	3
α-helix	450-451	2
β-strand	454-459	6	2
α-helix	461-463	3
α-helix	464-473	10
α-helix	479-481	3
β-strand	483-488	6	2
α-helix	499-511	13
α-helix	514-516	3
β-strand	519-521	3	3
β-strand	529-531	3	3
α-helix	533-537	5
α-helix	541-557	17
β-strand	566	1	3
α-helix	568-574	7
α-helix	577-579	3
α-helix	581-583	3
α-helix	584-587	4
α-helix	589-595	7
β-strand	609-610	2	4
β-strand	612-617	6	5
β-strand	620-625	6	5
β-strand	634-635	2	4
α-helix	640-648	9
α-helix	649-653	5
α-helix	654-656	3
α-helix	657-667	11
α-helix	673-676	4
α-helix	681-689	9
β-strand	691	1	6
α-helix	696-701	6
β-strand	703-706	4	7
α-helix	713-724	12
α-helix	727-737	11
β-strand	743	1	6
α-helix	747-750	4
β-strand	752	1	8
β-strand	757	1	8
β-strand	760-763	4	7
α-helix	771-772	2
β-strand	773-775	3	7
β-strand	780-782	3	7
α-helix	789-803	15

Chain B: 30 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	388-390	3
β-strand	393-397	5	9
β-strand	403-407	5	9
β-strand	412-414	3	9
α-helix	421-424	4
α-helix	430-444	15
α-helix	446-448	3
β-strand	451-460	10	10
α-helix	461-463	3
α-helix	464-473	10
α-helix	477-481	5
β-strand	482-489	8	10
α-helix	503-511	9
α-helix	514-516	3
β-strand	519-521	3	11
β-strand	529-531	3	11
α-helix	535-537	3
α-helix	541-557	17
β-strand	566	1	11
α-helix	568-575	8
α-helix	577-579	3
α-helix	581-583	3
α-helix	584-587	4
α-helix	591-600	10
β-strand	610	1	12
β-strand	612-617	6	13
β-strand	620-625	6	13
α-helix	630-632	3
β-strand	634	1	12
α-helix	642-648	7
α-helix	649-653	5
α-helix	654-656	3
α-helix	657-667	11
α-helix	673-676	4
α-helix	681-689	9
β-strand	691	1	14
α-helix	696-700	5
β-strand	703-704	2	15
α-helix	713-724	12
α-helix	727-738	12
β-strand	743	1	14
α-helix	748-750	3
β-strand	752	1	16
β-strand	757	1	16
β-strand	760-761	2	15
β-strand	764	1	17
α-helix	771-772	2
β-strand	773-775	3	15
α-helix	776-778	3
β-strand	780-782	3	15
β-strand	783	1	17
α-helix	789-802	14

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	109-114	6

Chain E: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	18
β-strand	12-14	3	18
β-strand	22	1	19
α-helix	23-34	12
β-strand	41-44	4	18
β-strand	55	1	19
β-strand	65-71	7	18

Chain F: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	20
β-strand	12-16	5	20
β-strand	22	1	21
α-helix	23-34	12
β-strand	41-44	4	20
β-strand	49	1	20
β-strand	55	1	21
β-strand	67-71	5	20
β-strand	74	1	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RSP5	A, B	protein	432	Saccharomyces cerevisiae	P39940 (AlphaFold model)
Protein SNA3	C, D	protein	24	Saccharomyces cerevisiae	P14359 (AlphaFold model)
Ubiquitin	E, F	protein	83	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4LCD_1 E3 ubiquitin-protein ligase RSP5 (chains A, B)
GSGGSVSQLGPLPSGWEMRLTNTARVYFVDHNTKTTTWDDPRLPSSLDQNVPQYKRDFRR
KVIYFRSQPALRILPGQLHIKVRRKNIFEDAYQEIMRQTPEDLKKRLMIKFDGEEGLDYG
GVSREFFFLLSHEMFNPFYGLFEYSAYDNYTIQINPNSGINPEHLNYFKFIGRVVGLGVF
HRRFLDAFFVGALYKMMLRKKVVLQDMEGVDAEVYNSLNWMLENSIDGVLDLTFSADDER
FGEVVTVDLKPDGRNIEVTDGNKKEYVELYTQWRIVDRVQEQFKAFMDGFNELIPEDLVT
VFDERELELLIGGIAEIDIEDWKKHTDYRGYQESDEVIQWFWKAVSEWDNEQRARLLQFT
TGTSRIPVNGFKDLQGSDGPRRFTIEKAGEVQQLPKSHTCFNRVDLPQYVDYDSMKQKLT
LAVEETIGFGQE

Sequence of entity 2 (C, D), FASTA

>4LCD_2 Protein SNA3 (chains C, D)
AQPPAYDEDDEAGADVPLMDNAQQ

Sequence of entity 3 (E, F), FASTA

>4LCD_3 Ubiquitin (chains E, F)
MGHHHHHHMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLED
GRTLSDYNIQKESTLHLVLRLRC

Primary citation

Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3. Kamadurai, H.B., Qiu, Y., Deng, A. et al. Elife (2013) 2:e00828-e00828. DOI 10.7554/eLife.00828 · PubMed

Other PDB entries of the same protein (UniProt P39940 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5HPL 2.31 Å, System-wide modulation of HECT E3 ligases with selective ubiquitin variant probes: Rsp5…
3OLM 2.5 Å, Structure and Function of a Ubiquitin Binding Site within the Catalytic Domain of a HECT…

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