2YHO: E3 ubiquitin-protein ligase mylip

Name: PDB 2YHO: The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor
Published: 2011-06-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor. Determined by X-ray diffraction at 2.1 Å resolution. Released 29 Jun 2011.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: HOMO SAPIENS
Chains: 8
Atoms: 7,208
Mol. weight: 103.5 kDa
Ligands: ZN
Released: 29 Jun 2011

Explore 2YHO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YHO contains 43 α-helices and 66 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	374-384	11
β-strand	386	1	1
β-strand	394	1	1
α-helix	395	1
β-strand	397-400	4	2
β-strand	404	1	3
β-strand	407	1	2
α-helix	409-412	4
β-strand	417	1	4
β-strand	424	1	4
β-strand	427-430	4	2
β-strand	432	1	5

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	17-18	2
β-strand	21-25	5	6
β-strand	32-38	7	6
α-helix	39-40	2
β-strand	49-55	7	6
β-strand	66-69	4	6
β-strand	75	1	7
β-strand	78	1	7
β-strand	83	1	6
β-strand	84	1	7
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain C: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	374-384	11
β-strand	386	1	8
β-strand	394	1	8
α-helix	395	1
β-strand	397-400	4	9
β-strand	404	1	5
β-strand	407	1	9
α-helix	409-412	4
β-strand	417	1	10
α-helix	423	1
β-strand	424	1	10
α-helix	425	1
β-strand	427-430	4	9
β-strand	432	1	3

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	17-18	2
β-strand	21-26	6	11
β-strand	29-38	10	11
α-helix	39-40	2
β-strand	49-55	7	11
β-strand	66-69	4	11
β-strand	75	1	12
β-strand	78	1	12
β-strand	83	1	11
β-strand	84	1	12
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain E: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	375-384	10
β-strand	386	1	13
β-strand	394	1	13
α-helix	395	1
β-strand	397-400	4	14
β-strand	404	1	15
β-strand	407	1	14
α-helix	409-412	4
β-strand	417	1	16
β-strand	424	1	16
β-strand	427-430	4	14
β-strand	432	1	17

Chain F: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	17-18	2
β-strand	21-26	6	18
β-strand	29-38	10	18
α-helix	39-40	2
β-strand	49-55	7	18
β-strand	66-69	4	18
β-strand	75	1	19
β-strand	78	1	19
β-strand	84	1	19
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Chain G: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	375-384	10
β-strand	386	1	20
β-strand	394	1	20
α-helix	395	1
β-strand	397-400	4	21
β-strand	404	1	17
β-strand	407	1	21
α-helix	409-413	5
β-strand	417	1	22
β-strand	424	1	22
β-strand	427-430	4	21
β-strand	432	1	15

Chain H: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	17-18	2
β-strand	21-25	5	23
β-strand	32-38	7	23
α-helix	39-40	2
β-strand	49-55	7	23
α-helix	64-65	2
β-strand	66-69	4	23
β-strand	78	1	24
β-strand	83	1	23
β-strand	84	1	24
α-helix	87-89	3
α-helix	99-111	13
α-helix	121-129	9
α-helix	131-145	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase mylip	A, C, E, G	protein	79	HOMO SAPIENS	Q8WY64 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 D1	B, D, F, H	protein	149	HOMO SAPIENS	P51668 (AlphaFold model)

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

>2YHO_1 E3 UBIQUITIN-PROTEIN LIGASE MYLIP (chains A, C, E, G)
GAQQTRVLQEKLRKLKEAMLCMVCCEEEINSTFCPCGHTVCCESCAAQLQSCPVCRSRVE
HVQHVYLPTHTSLLNLTVI

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

>2YHO_2 UBIQUITIN-CONJUGATING ENZYME E2 D1 (chains B, D, F, H)
GAMALKRIQKELSDLQRDPPAHCSAGPVGDDLFHWQATIMGPPDSAYQGGVFFLTVHFPT
DYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDP
LVPDIAQIYKSDKEKYNRHAREWTQKYAM

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

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

Primary citation

The Idol-Ube2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor. Zhang, L., Fairall, L., Goult, B.T. et al. Genes Dev (2011) 25:1262. DOI 10.1101/GAD.2056211 · PubMed

Other PDB entries of the same protein (UniProt Q8WY64 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SA1 1.06 Å, The RING domain of IDOL
9SA2 1.1 Å, The RING domain of IDOL
13SY 1.29 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with POB0041
13SQ 1.3 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z369936976
13SL 1.34 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z275151340
13SX 1.36 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with POB0134
13ST 1.37 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z608065044
13SW 1.37 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with POB0087
13SM 1.4 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z275179946
13SE 1.44 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z1587220559
13SN 1.44 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z2757439080
13SJ 1.47 Å, PanDDA analysis group deposition -- IDOL RING domain in complex with Z2643472210

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