7OJX: E3 ubiquitin-protein ligase RNF38

Name: PDB 7OJX: E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked Ub chain synthesis
Published: 2022-01-12
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked Ub chain synthesis. Determined by X-ray diffraction at 2.4 Å resolution. Released 12 Jan 2022.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 5
Atoms: 3,739
Mol. weight: 57.99 kDa
Ligands: ZN, ME7
Released: 12 Jan 2022

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

Secondary structure: helices and β-sheets

7OJX contains 20 α-helices and 38 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: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	398-400	3	1
β-strand	412-413	2	2
β-strand	418-419	2	2
α-helix	424	1
β-strand	425-428	4	1
β-strand	434-436	3	1
α-helix	437-446	10
β-strand	449	1	3
β-strand	456	1	3

Chain B: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	5-16	12
β-strand	27-31	5	4
β-strand	38-44	7	4
α-helix	45-46	2
β-strand	55-61	7	4
α-helix	70-71	2
β-strand	72-75	4	4
β-strand	81	1	5
β-strand	84	1	5
β-strand	90	1	4
β-strand	91	1	5
β-strand	93	1	6
α-helix	94-96	3
α-helix	106-117	12
α-helix	128-136	9
α-helix	138-153	16
α-helix	160-171	12
α-helix	176-185	10
α-helix	190-198	9

Chain C: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
β-strand	12-16	5	7
β-strand	22	1	8
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	8
β-strand	66-71	6	7
β-strand	75	1	6

Chain D: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	9
β-strand	12-16	5	9
β-strand	22	1	10
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	9
β-strand	48-49	2	9
α-helix	50-51	2
β-strand	55	1	10
α-helix	57-59	3
β-strand	66-71	6	9

Chain E: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	11
β-strand	12-16	5	11
β-strand	22	1	12
α-helix	23-34	12
β-strand	41-45	5	11
β-strand	48-49	2	11
β-strand	55	1	12
β-strand	66-71	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase RNF38	A	protein	79	Homo sapiens	Q9H0F5 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 K	B	protein	202	Homo sapiens	P61086 (AlphaFold model)
Polyubiquitin-B	C	protein	79	Homo sapiens	P0CG47 (AlphaFold model)
Polyubiquitin-B	D	protein	76	Homo sapiens	P0CG47 (AlphaFold model)
Polyubiquitin-B	E	protein	76	Homo sapiens	P0CG47 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7OJX_1 E3 ubiquitin-protein ligase RNF38 (chains A)
GSTKADIEQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKA
NRTCPICRADASEVHRDSE

Sequence of entity 2 (B), FASTA

>7OJX_2 Ubiquitin-conjugating enzyme E2 K (chains B)
GSMANIAVQRIKREFKEVLKSEETSKNQIKVDLVDENFTELRGEIAGPPDTPYEGGRYQL
EIKIPETYPFNPPKVRFITKIWHPNISSVTGAIKLDILRDQWAAAMTLRTVLLSLQALLA
AAEPDCPQDAVVANQYKQNPEMFKQTARLWAHVYAGAPVSSPEYTKKIENLSAMGFDRNA
VIVALSSKSWDVETATELLLSN

Sequence of entity 3 (C), FASTA

>7OJX_3 Polyubiquitin-B (chains C)
GGSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS
DYNIQKESTLHLVLRLRGG

Sequence of entity 4 (D), FASTA

>7OJX_4 Polyubiquitin-B (chains D)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGCQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Sequence of entity 5 (E), FASTA

>7OJX_5 Polyubiquitin-B (chains E)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
ME7	1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)	C10 H8 N2 O4	1

Primary citation

Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension. Nakasone, M.A., Majorek, K.A., Gabrielsen, M. et al. Nat Chem Biol (2022) 18:422-431. DOI 10.1038/s41589-021-00952-x · PubMed

Other PDB entries of the same protein (UniProt Q9H0F5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9Q88 1.2 Å, High-resolution structure of RNF38 RING domain
4V3L 1.53 Å, RNF38-UB-UbcH5B-Ub complex
4V3K 2.04 Å, RNF38-UbcH5B-UB complex
9Q8Y 2.63 Å, Structure of RNF38 RING with linchpin mutant R454Y in complex with Ubch5B-Ub
1X4J Solution structure of RING finger in RING finger protein 38

Browse structure collections

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