8EAZ: HOIL-1/E2-Ub/Ub transthiolation complex

Name: PDB 8EAZ: HOIL-1/E2-Ub/Ub transthiolation complex
Published: 2023-01-18
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

HOIL-1/E2-Ub/Ub transthiolation complex. Determined by X-ray diffraction at 3.08 Å resolution. Released 18 Jan 2023.

Method: X-ray diffraction
Resolution: 3.08 Å
Organism: Homo sapiens
Chains: 8
Atoms: 8,813
Mol. weight: 135.02 kDa
Ligands: ZN
Released: 18 Jan 2023

Explore 8EAZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EAZ contains 36 α-helices and 88 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: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	258-261	4
α-helix	264-268	5
β-strand	275	1	1
β-strand	280-281	2	2
β-strand	288-289	2	2
β-strand	295-296	2	1
β-strand	303-304	2	1
α-helix	306-314	9
β-strand	322	1	3
β-strand	326	1	4
β-strand	331	1	4
β-strand	335	1	3
α-helix	338-342	5
α-helix	347-364	18
β-strand	368-370	3	5
β-strand	379-381	3	5
β-strand	388-390	3	6
β-strand	397-399	3	6
β-strand	404-405	2	6
α-helix	411-423	13
α-helix	426-440	15
β-strand	445-446	2	7
β-strand	453-457	5	7
β-strand	462-464	3	8
β-strand	471-473	3	8
β-strand	478-479	2	8
β-strand	497	1	9
β-strand	500	1	9

Chain B: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	275	1	10
β-strand	280-281	2	11
β-strand	288-289	2	11
β-strand	295-296	2	10
β-strand	303-304	2	10
α-helix	306-314	9
β-strand	322	1	12
β-strand	326	1	13
β-strand	331	1	13
β-strand	335	1	12
α-helix	338-342	5
α-helix	347-364	18
β-strand	368-370	3	14
β-strand	379-381	3	14
β-strand	388-390	3	15
β-strand	397-399	3	15
β-strand	404-405	2	15
α-helix	411-423	13
α-helix	426-440	15
β-strand	445-446	2	16
β-strand	453-457	5	16
β-strand	462-464	3	17
β-strand	471-473	3	17
β-strand	478-479	2	17
β-strand	497	1	18
β-strand	500	1	18

Chain C: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
β-strand	22-27	6	19
β-strand	34-39	6	19
β-strand	51-56	6	19
β-strand	67-70	4	19
β-strand	76	1	20
β-strand	79	1	20
β-strand	84	1	19
β-strand	85	1	20
α-helix	88-90	3
α-helix	101-113	13
α-helix	123-131	9
α-helix	133-147	15

Chain D: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
β-strand	22-26	5	21
β-strand	34-39	6	21
β-strand	51-56	6	21
β-strand	67-70	4	21
β-strand	76	1	22
β-strand	79	1	22
β-strand	84	1	21
β-strand	85	1	22
α-helix	88-90	3
α-helix	101-113	13
α-helix	123-130	8
α-helix	133-147	15

Chain E: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	12-16	5	7
β-strand	22	1	23
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	7
β-strand	48-49	2	7
α-helix	50-51	2
β-strand	55	1	23
α-helix	57-59	3
β-strand	66-74	9	7
α-helix	75	1

Chain F: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	16
β-strand	12-16	5	16
β-strand	22	1	24
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	16
β-strand	48-49	2	16
α-helix	50-51	2
β-strand	55	1	24
β-strand	66-74	9	16

Chains G and H: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	25
β-strand	12-16	5	25
β-strand	22	1	26
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	25
β-strand	48-49	2	25
α-helix	50-51	2
β-strand	55	1	26
β-strand	66-71	6	25
β-strand	72	1	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RanBP-type and C3HC4-type zinc finger-containing protein 1	A, B	protein	280	Homo sapiens	Q9BYM8 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 L3	C, D	protein	157	Homo sapiens	P68036 (AlphaFold model)
Ubiquitin	E, F, G, H	protein	76	Homo sapiens	P0CG48 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8EAZ_1 RanBP-type and C3HC4-type zinc finger-containing protein 1 (chains A, B)
GPDEEERARLAGEEEALRQYQQRKQQQQEGNYLQHVQLDQRSLVLNTEPAECPVCYSVLA
PGEAVVLRECLHTFCRECLQGTIRNSQEAEVSCPFIDNTYSCSGKLLEREIKALLTPEDY
QRFLDLGISIAENRSAFSYHCKTPDCKGWCFFEDDVNEFTCPVCFHVNCLLCKAIHEQMN
CKEYQEDLALRAQNDVAARQTTEMLKVMLQQGEAMRCPQCQIVVQKKDGADWIRCTVCHT
EICWVTKGPRWGPGGPGDTSGGCRCRVNGIPCHPSCQNCH

Sequence of entity 2 (C, D), FASTA

>8EAZ_2 Ubiquitin-conjugating enzyme E2 L3 (chains C, D)
GPGMAASRRLMKELEEIRKCGMKNFRNIQVDEANLLTWQGLIVPDNPPYDKGAFRIEINF
PAEYPFKPPKITFKTKIYHPNIDEKGQVKLPVISAENWKPATKTDQVIQSLIALVNDPQP
EHPLRADLAEEYSKDRKKFCKNAEEFTKKYGEKRPVD

Sequence of entity 3 (E, F, G, H), FASTA

>8EAZ_3 Ubiquitin (chains E, F, G, H)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	14

Primary citation

The unifying catalytic mechanism of the RING-between-RING E3 ubiquitin ligase family. Wang, X.S., Cotton, T.R., Trevelyan, S.J. et al. Nat Commun (2023) 14:168-168. DOI 10.1038/s41467-023-35871-z · PubMed

Other PDB entries of the same protein (UniProt Q9BYM8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8K6Q 1.59 Å, Crystal structure of HOIL-1L LTM domain
9EGW 1.78 Å, HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled)
7YUJ 1.86 Å, Crystal structure of HOIL-1L(365-510)
7V8E 1.9 Å, Crystal structure of IpaH1.4 LRR domain bound to HOIL-1L UBL domain.
9EGV 2.0 Å, HOIL-1 RING2 domain bound to ubiquitin
8BVL 2.24 Å, Crystal structure of the IBR-RING2 domain of HOIL-1
7YUI 2.6 Å, Crystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin
4DBG 2.71 Å, Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative
2CRC Solution structure of the zf-RanBP domain of the protein HBV associated factor
2LGY Ubiquitin-like domain from HOIL-1

Browse structure collections

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